After the quick installation, the docker container created does not start.

[kazusadna]

After executing quickinstall using HapCHAT's Dockerfile, I tried to start up and connect the created Docker container.

Although "docker start" was executed and it seemed that the container started, when trying to connect to the container with "docker attach", an error message is displayed and connection can not be made.

The following code is the work log.

`# docker run -v /root/HapCHAT:/data algolab/hapchat
Unable to find image 'algolab/hapchat:latest' locally
Trying to pull repository docker.io/algolab/hapchat ...
latest: Pulling from docker.io/algolab/hapchat

1be7f2b886e8: Pulling fs layer
6fbc4a21b806: Pulling fs layer
c71a6f8e1378: Pulling fs layer
4be3072e5a37: Pulling fs layer
06c6d2f59700: Pulling fs layer
4708070b1207: Pulling fs layer
936f29c876d6: Pulling fs layer

(ommision)

Status: Downloaded newer image for docker.io/algolab/hapchat:latest
Nothing to be done.
# docker iamages REPOSITORY TAG IMAGE ID CREATED SIZE docker.io/algolab/hapchat latest b3e7d09db905 5 months ago 1.13 GB
# docker ps -a CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES a218d5b80ede algolab/hapchat "/usr/bin/snakemake" 4 minutes ago Exited (0) 4 minutes ago hardcore_boyd
# docker start a218d5b80ede
a218d5b80ede
# docker attach a218d5b80ede
You cannot attach to a stopped container, start it first

Is there a way to solve this phenomenon?

Above, thank you.

[gdv]

Can you post the contents of the /root/HapCHAT directory? The output should be there. Best Gianluca Della Vedova https://gianluca.dellavedova.org Il Mer 8 Ago 2018, 04:28 kazusadna <notifications@github.com> ha scritto:

…

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[kazusadna]

Thank you for your reply.

The contents of / root / HapCHAT are as follows.

`# ls -la

total 3951824
drwxr-xr-x 9 root root 4096 7 31 16:25 .
dr-xr-x---. 36 root root 4096 7 31 16:08 ..
drwxr-xr-x 4 root root 4096 7 31 16:25 .file.bam.hx_
-rw-r--r-- 1 root root 18 7 26 02:51 CNAME
-rw-r--r-- 1 root root 6928 7 26 02:51 HapCHAT.py
-rw-r--r-- 1 root root 35141 7 26 02:51 LICENSE
-rw-r--r-- 1 root root 47 7 31 16:10 MD5SUM
-rw-r--r-- 1 root root 614 7 26 02:51 README.md
-rw-r--r-- 1 root root 26 7 26 02:51 _config.yml
drwxr-xr-x 2 root root 23 7 31 16:08 docker
drwxr-xr-x 2 root root 51 7 31 16:08 docs
drwxr-xr-x 2 root root 65 7 31 16:08 example
drwxr-xr-x 4 root root 63 7 31 16:08 experiments
-rw-r--r-- 1 root root 668740 7 31 16:10 file.bam
-rw-r--r-- 1 root root 5240 7 31 16:23 file.bam.bai
-rw-r--r-- 1 root root 49171 7 31 16:10 file.vcf
-rw-r--r-- 1 root root 3153506519 7 31 16:22 genome.fasta
-rw-r--r-- 1 root root 2746 7 31 16:24 genome.fasta.fai
-rw-r--r-- 1 root root 892331003 7 31 16:22 genome.fasta.gz
-rw-r--r-- 1 root root 0 7 31 16:25 out.phased.vcf
-rw-r--r-- 1 root root 0 7 31 16:23 out.realigned.phased.vcf
drwxr-xr-x 2 root root 136 7 31 16:08 scripts
-rw-r--r-- 1 root root 1882 7 26 02:51 setup.sh
drwxr-xr-x 2 root root 4096 7 31 16:08 src`

Please reply if there is any other necessary information.

Above, thank you.

[gdv]

The results should be in the out.phased.vcf file, but it seems that it's empty

Do you have a .file.bam.hx_ directory inside /root/HapCHAT ? In case, can you paste the contents on any of file there?

[kazusadna]

Thank you for your reply.

The contents of the .file.bam.hx_ directory are as follows.

`# ls -la
total 3951824
drwxr-xr-x 9 root root 4096 7 31 16:25 .
dr-xr-x---. 36 root root 4096 7 31 16:08 ..
drwxr-xr-x 4 root root 4096 7 31 16:25 .file.bam.hx_
-rw-r--r-- 1 root root 18 7 26 02:51 CNAME
-rw-r--r-- 1 root root 6928 7 26 02:51 HapCHAT.py
-rw-r--r-- 1 root root 35141 7 26 02:51 LICENSE
-rw-r--r-- 1 root root 47 7 31 16:10 MD5SUM
-rw-r--r-- 1 root root 614 7 26 02:51 README.md
-rw-r--r-- 1 root root 26 7 26 02:51 _config.yml
drwxr-xr-x 2 root root 23 7 31 16:08 docker
drwxr-xr-x 2 root root 51 7 31 16:08 docs
drwxr-xr-x 2 root root 65 7 31 16:08 example
drwxr-xr-x 4 root root 63 7 31 16:08 experiments
-rw-r--r-- 1 root root 668740 7 31 16:10 file.bam
-rw-r--r-- 1 root root 5240 7 31 16:23 file.bam.bai
-rw-r--r-- 1 root root 49171 7 31 16:10 file.vcf
-rw-r--r-- 1 root root 3153506519 7 31 16:22 genome.fasta
-rw-r--r-- 1 root root 2746 7 31 16:24 genome.fasta.fai
-rw-r--r-- 1 root root 892331003 7 31 16:22 genome.fasta.gz
-rw-r--r-- 1 root root 0 7 31 16:25 out.phased.vcf
-rw-r--r-- 1 root root 0 7 31 16:23 out.realigned.phased.vcf
drwxr-xr-x 2 root root 136 7 31 16:08 scripts
-rw-r--r-- 1 root root 1882 7 26 02:51 setup.sh
drwxr-xr-x 2 root root 4096 7 31 16:08 src

cd .file.bam.hx_

ls -l

total 96
-rw-r--r-- 1 root root 466 7 31 16:25 raw.wif
drwxr-xr-x 2 root root 138 7 31 16:25 raw.wif.info_
-rw-r--r-- 1 root root 1616 7 31 16:25 raw.wif.log
-rw-r--r-- 1 root root 359 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif
-rw-r--r-- 1 root root 359 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif
-rw-r--r-- 1 root root 1231 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.log
-rw-r--r-- 1 root root 0 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf
-rw-r--r-- 1 root root 270 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf.log
-rw-r--r-- 1 root root 4 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.graph
-rw-r--r-- 1 root root 6 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.lines
-rw-r--r-- 1 root root 6 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.lines.shuf1
-rw-r--r-- 1 root root 1034 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.log
-rw-r--r-- 1 root root 6 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.sample_s1_m15
-rw-r--r-- 1 root root 0 7 31 16:25 raw.wif.merged_e15_m25_t6_n3.wif.sample_s1_m15.log
-rw-r--r-- 1 root root 352 7 31 16:25 raw.wif.transcript
-rw-r--r-- 1 root root 474 7 31 16:25 realigned.wif
drwxr-xr-x 2 root root 138 7 31 16:25 realigned.wif.info_
-rw-r--r-- 1 root root 1660 7 31 16:25 realigned.wif.log
-rw-r--r-- 1 root root 381 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif
-rw-r--r-- 1 root root 381 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif
-rw-r--r-- 1 root root 1243 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.log
-rw-r--r-- 1 root root 0 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf
-rw-r--r-- 1 root root 276 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf.log
-rw-r--r-- 1 root root 4 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.graph
-rw-r--r-- 1 root root 6 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.lines
-rw-r--r-- 1 root root 6 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.lines.shuf1
-rw-r--r-- 1 root root 1040 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.log
-rw-r--r-- 1 root root 6 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.sample_s1_m15
-rw-r--r-- 1 root root 0 7 31 16:25 realigned.wif.merged_e15_m25_t6_n3.wif.sample_s1_m15.log
-rw-r--r-- 1 root root 352 7 31 16:25 realigned.wif.transcript

cat raw.wif.log

This is WhatsHap 0.13+52.g7b63430 running under Python 3.5.2
Working on 1 samples from 1 family
WARNING: The maximum coverage is too high! WhatsHap may take a long time to finish and require a huge amount of memory.
======== Working on chromosome '1'
---- Processing individual HG002
Using maximum coverage per sample of 1000X
Number of variants skipped due to missing genotypes: 0
Number of remaining heterozygous variants: 628
Reading alignments for sample 'HG002'and detecting alleles ...
Found 4 reads covering 11 variants
Kept 4 reads that cover at least two variants each
Reducing coverage to at most 1000X by selecting most informative reads ...
Selected 4 reads covering 11 variants
Best-case phasing would result in 1 non-singleton phased blocks (1 in total)
... after read selection: 1 non-singleton phased blocks (1 in total)
Variants covered by at least one phase-informative read in at least one individual after read selection: 11
Adding reads to be used for phasing in wif format to running dictionary
======== Writing VCF
Done writing VCF
Writing running dictionary of reads in wif format to '/data/.file.bam.hx_/raw.wif'

== SUMMARY ==
Maximum memory usage: 0.026 GB
Time spent reading BAM: 0.2 s
Time spent parsing VCF: 0.1 s
Time spent selecting reads: 0.0 s
Time spent phasing: 0.0 s
Time spent writing VCF: 0.2 s
Time spent finding components: 0.0 s
Time spent on rest: 0.1 s
Total elapsed time: 0.5 s

cat realigned.wif.log

This is WhatsHap 0.13+52.g7b63430 running under Python 3.5.2
BAM index not found, creating it now.
Working on 1 samples from 1 family
WARNING: The maximum coverage is too high! WhatsHap may take a long time to finish and require a huge amount of memory.
======== Working on chromosome '1'
---- Processing individual HG002
Using maximum coverage per sample of 1000X
Number of variants skipped due to missing genotypes: 0
Number of remaining heterozygous variants: 628
Reading alignments for sample 'HG002'and detecting alleles ...
Found 4 reads covering 11 variants
Kept 4 reads that cover at least two variants each
Reducing coverage to at most 1000X by selecting most informative reads ...
Selected 4 reads covering 11 variants
Best-case phasing would result in 1 non-singleton phased blocks (1 in total)
... after read selection: 1 non-singleton phased blocks (1 in total)
Variants covered by at least one phase-informative read in at least one individual after read selection: 11
Adding reads to be used for phasing in wif format to running dictionary
======== Writing VCF
Done writing VCF
Writing running dictionary of reads in wif format to '/data/.file.bam.hx_/realigned.wif'

== SUMMARY ==
Maximum memory usage: 0.521 GB
Time spent reading BAM: 4.3 s
Time spent parsing VCF: 0.1 s
Time spent selecting reads: 0.0 s
Time spent phasing: 0.0 s
Time spent writing VCF: 0.1 s
Time spent finding components: 0.0 s
Time spent on rest: 64.5 s
Total elapsed time: 69.0 s

cat realigned.wif.merged_e15_m25_t6_n3.wif.log

INFO [180731 072504] Program started.
INFO [180731 072504] Error Rate: 0.15
INFO [180731 072504] Max Error Rate: 0.25
INFO [180731 072504] Positive Threshold: 1000000
INFO [180731 072504] Negative Threshold: 1000
INFO [180731 072504] Started reading WIF file...
INFO [180731 072504] Finished reading WIF file.
INFO [180731 072504] N. WIF entries: 4
INFO [180731 072504] Blue Graph
INFO [180731 072504] Nodes: 4 - Edges: 1 - ConnComp: 3
INFO [180731 072504] Non-Blue Graph
INFO [180731 072504] Nodes: 4 - Edges: 2 - ConnComp: 2
INFO [180731 072504] Red Graph
INFO [180731 072504] Nodes: 4 - Edges: 0 - ConnComp: 4
INFO [180731 072504] Non-Red Graph
INFO [180731 072504] Nodes: 4 - Edges: 2 - ConnComp: 2
INFO [180731 072504] Started Merging Reads...
INFO [180731 072504] Printing graph in /data/.file.bam.hx_/realigned.wif.merged_e15_m25_t6_n3.wif.graph file
INFO [180731 072504] Finished Merging Reads.
INFO [180731 072504] Program Finshed

cat raw.wif.merged_e15_m25_t6_n3.wif.log

INFO [180731 072508] Program started.
INFO [180731 072508] Error Rate: 0.15
INFO [180731 072508] Max Error Rate: 0.25
INFO [180731 072508] Positive Threshold: 1000000
INFO [180731 072508] Negative Threshold: 1000
INFO [180731 072508] Started reading WIF file...
INFO [180731 072508] Finished reading WIF file.
INFO [180731 072508] N. WIF entries: 4
INFO [180731 072508] Blue Graph
INFO [180731 072508] Nodes: 4 - Edges: 1 - ConnComp: 3
INFO [180731 072508] Non-Blue Graph
INFO [180731 072508] Nodes: 4 - Edges: 2 - ConnComp: 2
INFO [180731 072508] Red Graph
INFO [180731 072508] Nodes: 4 - Edges: 0 - ConnComp: 4
INFO [180731 072508] Non-Red Graph
INFO [180731 072508] Nodes: 4 - Edges: 1 - ConnComp: 3
INFO [180731 072508] Started Merging Reads...
INFO [180731 072508] Printing graph in /data/.file.bam.hx_/raw.wif.merged_e15_m25_t6_n3.wif.graph file
INFO [180731 072508] Finished Merging Reads.
INFO [180731 072508] Program Finshed`

Above, thank you.

[murraypatterson]

Hello,

All of the above log files seem fine --- what is to be expected, so I suspect that the problem happened somewhere downstream from this. Could you post the contents of raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.log and raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf.log ? They seem not to be empty in your above directory listing

Thanks,
Murray

[kazusadna]

Thank you for your reply.

The contents of raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.log and raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf.log are as follows.

`# cat raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.log

• INFO (main :/HapCHAT.cpp:169 ) 07:25:08 | HapCHAT (master@269d4f8-dirty)
• INFO (main :/HapCHAT.cpp:173 ) 07:25:08 | Starting...
• INFO (main :/HapCHAT.cpp:180 ) 07:25:08 | Arguments:
• INFO (main :/HapCHAT.cpp:181 ) 07:25:08 | Initialized? True
• INFO (main :/HapCHAT.cpp:182 ) 07:25:08 | Input filename: '/data/.file.bam.hx_/raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif'
• INFO (main :/HapCHAT.cpp:183 ) 07:25:08 | Haplotype filename: '/data/.file.bam.hx_/raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap'
• INFO (main :/HapCHAT.cpp:184 ) 07:25:08 | Discard weights? False
• INFO (main :/HapCHAT.cpp:185 ) 07:25:08 | Do not add X's? False
• INFO (main :/HapCHAT.cpp:186 ) 07:25:08 | All-heterozygous assumption? True
• INFO (main :/HapCHAT.cpp:187 ) 07:25:08 | Input as unique block? False
• INFO (main :/HapCHAT.cpp:188 ) 07:25:08 | Error rate: 0.05
• INFO (main :/HapCHAT.cpp:189 ) 07:25:08 | Alpha: 0.1
• INFO (main :/HapCHAT.cpp:190 ) 07:25:08 | Balancing? True
• INFO (main :/HapCHAT.cpp:191 ) 07:25:08 | Balancing activates after coverage: 1000
• INFO (main :/HapCHAT.cpp:192 ) 07:25:08 | Balance ratio: 0`

`# cat raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf.log

Traceback (most recent call last):
File "/HapCHAT/scripts/subvcf.py", line 141, in
h0,h1 = load_haplotypes(open(a[i],'r'))
FileNotFoundError: [Errno 2] No such file or directory: '/data/.file.bam.hx_/raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap'`

Above, thank you.

[murraypatterson]

Ok thanks, it seems that the hapchat core algorithm is not outputting anything, since there is no raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap file present (as can be seen in the above directory listing), but this strange because it is doing it quitely, i.e., raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.log is incomplete, but contains no error messages. Could you post here the contents of raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif ?

Thanks again,
Murray

[kazusadna]

Thank you for your reply.

The contents of raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif are as follows.

`# cat raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif

9010254 G 0 17 : 9010807 G 0 19 : 9010984 G 0 19 : 9011046 G 0 25 : 9011537 G 0 26 : 9011586 G 0 24 : 9011722 G 0 13 : # X : X
9010254 C 1 12 : 9010570 C 1 4 : 9010807 C 1 9 : # X : X
9010254 C 1 13 : 9010570 C 1 11 : 9010984 G 0 1 : 9011046 G 0 6 : 9011537 C 1 4 : 9011586 C 1 10 : 9011722 C 1 13 : 9012776 C 1 14 : 9013096 G 0 10 : 9013970 C 1 13 : # X : X
`

Thank you for always responding quickly.

[murraypatterson]

Hi again,

Yes, that seems to be the expected input to the core algorithm, strange. Let's start from scratch, here is a transcript of what happens when I run HapCHAT from the docker image, according to the "Quick Install" instructions. Note that I first create an empty directory datadir, and then I run the algolab/hapchat image, linking this datadir with the image's /data, invoking a run on the example, whose output files we see here at the end

patterson@franklin:~$ mkdir datadir
patterson@franklin:~$ docker run -v /home/patterson/datadir/:/data algolab/hapchat
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	download_reference
	1	master
	1	run_hapchat
	1	run_hapchat_realignment
	3	transfer_file
	1	uncompress_reference
	8
rule transfer_file:
	input: MD5SUM
	output: /data/MD5SUM
1 of 8 steps (12%) done
rule transfer_file:
	input: file.bam
	output: /data/file.bam
2 of 8 steps (25%) done
rule transfer_file:
	input: file.vcf
	output: /data/file.vcf
3 of 8 steps (38%) done
rule download_reference:
	input: /data/MD5SUM
	output: /data/genome.fasta.gz
4 of 8 steps (50%) done
rule uncompress_reference:
	input: /data/genome.fasta.gz
	output: /data/genome.fasta
	log: /data/download.log

gzip: /data/genome.fasta.gz: decompression OK, trailing garbage ignored
5 of 8 steps (62%) done
rule run_hapchat_realignment:
	input: /data/genome.fasta, /data/file.bam, /data/file.vcf
	output: /data/out.realigned.phased.vcf
6 of 8 steps (75%) done
rule run_hapchat:
	input: /data/file.bam, /data/file.vcf
	output: /data/out.phased.vcf
7 of 8 steps (88%) done
localrule master:
	input: /data/out.phased.vcf, /data/out.realigned.phased.vcf
8 of 8 steps (100%) done
patterson@franklin:~$ cd datadir/
patterson@franklin:~/datadir$ ll
total 3951868
drwxrwxr-x  3 patterson patterson       4096 ago 14 20:31 .
drwxr-xr-x 86 patterson patterson       4096 ago 14 20:27 ..
-rw-r--r--  1 root      root          668740 ago 14 20:28 file.bam
-rw-r--r--  1 root      root            5240 ago 14 20:30 file.bam.bai
drwxr-xr-x  4 root      root            4096 ago 14 20:31 .file.bam.hx_
-rw-r--r--  1 root      root           49171 ago 14 20:28 file.vcf
-rw-r--r--  1 root      root      3153506519 ago 14 20:29 genome.fasta
-rw-r--r--  1 root      root            2746 ago 14 20:30 genome.fasta.fai
-rw-r--r--  1 root      root       892331003 ago 14 20:29 genome.fasta.gz
-rw-r--r--  1 root      root              47 ago 14 20:28 MD5SUM
-rw-r--r--  1 root      root           49292 ago 14 20:31 out.phased.vcf
-rw-r--r--  1 root      root           49259 ago 14 20:31 out.realigned.phased.vcf

what do you get when doing exactly as the above? Note that I captured all of this output with the unix script command, dumping this to a typescript file. The above is the contents of this typescript file.

Best,
Murray

[kazusadna]

Thank you for your reply.

Since uploading fails, we pasted the contents of typescript as it is.
The content is the same as the result you presented.

`The script is 16: 24: 30 seconds on August 15, 2018 Started on
[root@rh7MH ~]# mkdir HapCHATinst
[root@rh7MH ~]#
[root@rh7MH ~]# docker run -v /root/HapCHAT/:/data algolab/hapchat
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 download_reference
1 master
1 run_hapchat
1 run_hapchat_realignment
3 transfer_file
1 uncompress_reference
8
rule transfer_file:
input: MD5SUM
output: /data/MD5SUM
1 of 8 steps (12%) done
rule transfer_file:
input: file.bam
output: /data/file.bam
2 of 8 steps (25%) done
rule transfer_file:
input: file.vcf
output: /data/file.vcf
3 of 8 steps (38%) done
rule download_reference:
input: /data/MD5SUM
output: /data/genome.fasta.gz
4 of 8 steps (50%) done
rule uncompress_reference:
input: /data/genome.fasta.gz
output: /data/genome.fasta
log: /data/download.log

gzip: /data/genome.fasta.gz: decompression OK, trailing garbage ignored
5 of 8 steps (62%) done
rule run_hapchat_realignment:
input: /data/file.vcf, /data/genome.fasta, /data/file.bam
output: /data/out.realigned.phased.vcf
6 of 8 steps (75%) done
rule run_hapchat:
input: /data/file.vcf, /data/file.bam
output: /data/out.phased.vcf
7 of 8 steps (88%) done
localrule master:
input: /data/out.phased.vcf, /data/out.realigned.phased.vcf
8 of 8 steps (100%) done
[root@rh7MH ~]# cd HapCH�AT/
[root@rh7MH HapCHAT]# ll
合計 3951744
-rw-r--r-- 1 root root 47 8月 15 16:24 MD5SUM
-rw-r--r-- 1 root root 668740 8月 15 16:24 file.bam
-rw-r--r-- 1 root root 5240 8月 15 16:36 file.bam.bai
-rw-r--r-- 1 root root 49171 8月 15 16:24 file.vcf
-rw-r--r-- 1 root root 3153506519 8月 15 16:34 genome.fasta
-rw-r--r-- 1 root root 2746 8月 15 16:38 genome.fasta.fai
-rw-r--r-- 1 root root 892331003 8月 15 16:34 �[0m�[01;31mgenome.fasta.gz�[0m
-rw-r--r-- 1 root root 0 8月 15 16:38 out.phased.vcf
-rw-r--r-- 1 root root 0 8月 15 16:36 out.realigned.phased.vcf
[root@rh7MH HapCHAT]# exit
exit

The script is written on August 15, 2018 at 16:43:35 Finished in
`

Thank you for always responding quickly.

[murraypatterson]

Hi,

Just one note: in the line [root@rh7MH ~]# docker run -v /root/HapCHAT/:/data algolab/hapchat, I think you meant to link the newly created HapCHATinst directory, created with [root@rh7MH ~]# mkdir HapCHATinst and not /root/HapCHAT/

Best,
Murray

[kazusadna]

Thank you for your reply.

Sorry, the pasted log was incorrect. This is correct.

`The script is 16: 24: 30 seconds on August 15, 2018 Started on
[root@rh7MH ~]# mkdir HapCHAT
[root@rh7MH ~]#
[root@rh7MH ~]# docker run -v /root/HapCHAT/:/data algolab/hapchat
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 download_reference
1 master
1 run_hapchat
1 run_hapchat_realignment
3 transfer_file
1 uncompress_reference
8
rule transfer_file:
input: MD5SUM
output: /data/MD5SUM
1 of 8 steps (12%) done
rule transfer_file:
input: file.bam
output: /data/file.bam
2 of 8 steps (25%) done
rule transfer_file:
input: file.vcf
output: /data/file.vcf
3 of 8 steps (38%) done
rule download_reference:
input: /data/MD5SUM
output: /data/genome.fasta.gz
4 of 8 steps (50%) done
rule uncompress_reference:
input: /data/genome.fasta.gz
output: /data/genome.fasta
log: /data/download.log

gzip: /data/genome.fasta.gz: decompression OK, trailing garbage ignored
5 of 8 steps (62%) done
rule run_hapchat_realignment:
input: /data/file.vcf, /data/genome.fasta, /data/file.bam
output: /data/out.realigned.phased.vcf
6 of 8 steps (75%) done
rule run_hapchat:
input: /data/file.vcf, /data/file.bam
output: /data/out.phased.vcf
7 of 8 steps (88%) done
localrule master:
input: /data/out.phased.vcf, /data/out.realigned.phased.vcf
8 of 8 steps (100%) done
[root@rh7MH ~]# cd HapCH�AT/
[root@rh7MH HapCHAT]# ll
total 3951744
-rw-r--r-- 1 root root 47 8 15 16:24 MD5SUM
-rw-r--r-- 1 root root 668740 8 15 16:24 file.bam
-rw-r--r-- 1 root root 5240 8 15 16:36 file.bam.bai
-rw-r--r-- 1 root root 49171 8 15 16:24 file.vcf
-rw-r--r-- 1 root root 3153506519 8 15 16:34 genome.fasta
-rw-r--r-- 1 root root 2746 8 15 16:38 genome.fasta.fai
-rw-r--r-- 1 root root 892331003 8 15 16:34 �[0m�[01;31mgenome.fasta.gz�[0m
-rw-r--r-- 1 root root 0 8 15 16:38 out.phased.vcf
-rw-r--r-- 1 root root 0 8 15 16:36 out.realigned.phased.vcf
[root@rh7MH HapCHAT]# exit
exit

The script is written on August 15, 2018 at 16:43:35 Finished in
`

Above, thank you.

[gdv]

That is weird. Let's try to check even trivial things. Can you please post the output of docker -v and of df -h, please?
Can you also write which OS (and version) are you using?

[kazusadna]

Hello,

The output results of docker -v and df -h are as follows.

`[root@rh7MH ~]# docker -v
Docker version 1.13.1, build dded712/1.13.1

[root@rh7MH ~]# df -h
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/centos-root 37G 22G 15G 61% /
devtmpfs 1.9G 0 1.9G 0% /dev
tmpfs 1.9G 0 1.9G 0% /dev/shm
tmpfs 1.9G 9.0M 1.9G 1% /run
tmpfs 1.9G 0 1.9G 0% /sys/fs/cgroup
/dev/sda1 497M 310M 187M 63% /boot
tmpfs 380M 0 380M 0% /run/user/0
tmpfs 380M 0 380M 0% /run/user/1001
`

Also, the OS version is as follows.

`
[root@rh7MH ~]# uname -a
Linux rh7MH 3.10.0-862.9.1.el7.x86_64 #1 SMP Mon Jul 16 16:29:36 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

[root@rh7MH ~]# cat /etc/redhat-release
CentOS Linux release 7.5.1804 (Core)
`

Above, thank you.

[gdv]

Thanks, I have tried to replicate the problem in a CentOS VM, and I have got a problem that is very similar to yours (not exactly the same, but I think the cause is the same).
The reason should be https://stackoverflow.com/questions/24288616/permission-denied-on-accessing-host-directory-in-docker and consists of an interaction between docker and the SElinux configuration.

Please try docker run -v /root/HapCHAT/:/data:Z algolab/hapchat (notice the Z), possibly in a new directory `/root/HapCHAT: in my VM it worked.

Thanks for your help