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marbl / MetaCompass

MetaCompass: Reference-guided Assembly of Metagenomes
https://github.com/marbl/MetaCompass/wiki
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Error in job reference_recruitment while creating output files #9

Closed bharat1912 closed 5 years ago

bharat1912 commented 5 years ago

  1. Installed metaCompass v 1.3 (github version in conda in py3.5 env)

  2. Tested installation using: Reference-guided assembly with known reference genomes (no reference selection). Completed without erros

  3. Ran Reference-guided assembly with reference selection with own samples copied to dir tutorial: (8010015 seqs, length 300) $python3 go_metacompass.py -P tutorial/CS1BS_ATBW8_GCCAAT_L001_R1.fastq,tutorial/CS1BS_ATBW8_GCCAAT_L001_R2.fastq -l 300 -o CS1BS.output

  4. Created error as follows (tried a few things e.g. downgraded snakeman to 3.11) but none worked. Assistance in trouble shooting appreciated checking for dependencies (Bowtie2, Blast, kmermask, Snakemake, etc) /home/bharat/opt/anaconda3/envs/py35/bin/snakemake Snakemake--->[OK] Bowtie2--->[OK] /home/bharat/opt/anaconda3/envs/py35/bin/blastn Blast+--->[OK] /home/bharat/opt/anaconda3/envs/py35/bin/kmer-mask kmer-mask--->[OK] /usr/bin/mash mash--->[OK] Provided cores: 1 Rules claiming more threads will be scaled down. Job counts: count jobs 1 all 1 assemble_unmapped 1 bam_sort 1 bowtie2_map 1 build_contigs 1 create_tsv 1 fastq2fasta 1 join_contigs 1 kmer_mask 1 merge_reads 1 pilon_contigs 1 pilon_map 1 reference_recruitment 1 sam_to_bam 14 Resources before job selection: {'_nodes': 9223372036854775807, '_cores': 1} Ready jobs (1): merge_reads Selected jobs (1): merge_reads Resources after job selection: {'_nodes': 9223372036854775806, '_cores': 0}

---merge fastq reads Reason: Missing output files: CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq

Releasing 1 _nodes (now 9223372036854775807). Releasing 1 _cores (now 1). Finished job 10. 1 of 14 steps (7%) done Resources before job selection: {'_nodes': 9223372036854775807, '_cores': 1} Ready jobs (1): kmer_mask Selected jobs (1): kmer_mask Resources after job selection: {'_nodes': 9223372036854775806, '_cores': 0}

---kmer-mask fastq Reason: Missing output files: CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.marker.match.1.fastq; Input files updated by another job: CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq

Releasing 1 _nodes (now 9223372036854775807). Releasing 1 _cores (now 1). Finished job 13. 2 of 14 steps (14%) done Resources before job selection: {'_nodes': 9223372036854775807, '_cores': 1} Ready jobs (1): fastq2fasta Selected jobs (1): fastq2fasta Resources after job selection: {'_nodes': 9223372036854775806, '_cores': 0}

---Converting fastq to fasta. Reason: Missing output files: CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.fasta; Input files updated by another job: CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.marker.match.1.fastq

Releasing 1 _nodes (now 9223372036854775807). Releasing 1 _cores (now 1). Finished job 11. 3 of 14 steps (21%) done Resources before job selection: {'_nodes': 9223372036854775807, '_cores': 1} Ready jobs (1): reference_recruitment Selected jobs (1): reference_recruitment Resources after job selection: {'_nodes': 9223372036854775806, '_cores': 0}

---reference recruitment. Reason: Missing output files: CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out/mc.refseq.fna; Input files updated by another job: CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq, CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.fasta

Full Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/py35/lib/python3.5/site-packages/snakemake/executors.py", line 848, in run_wrapper version, rule, conda_env) File "/home/bharat/opt/anaconda3/envs/py35/MetaCompass/snakemake/metacompass.iter0.paired.py", line 168, in __rule_reference_recruitment sam=rules.pilon_map.output.sam File "/home/bharat/opt/anaconda3/envs/py35/lib/python3.5/site-packages/snakemake/shell.py", line 80, in new raise sp.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'mkdir -p CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out; python3 /home/bharat/opt/anaconda3/envs/py35/MetaCompass/bin/select_references.py tax CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.fasta CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out 1 2 1>> CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log 2>&1' returned non-zero exit status 1

Error in job reference_recruitment while creating output files CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out/mc.refseq.ids, CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out, CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out/mc.refseq.fna. Full Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/py35/lib/python3.5/site-packages/snakemake/executors.py", line 848, in run_wrapper version, rule, conda_env) File "/home/bharat/opt/anaconda3/envs/py35/MetaCompass/snakemake/metacompass.iter0.paired.py", line 168, in __rule_reference_recruitment sam=rules.pilon_map.output.sam File "/home/bharat/opt/anaconda3/envs/py35/lib/python3.5/site-packages/snakemake/shell.py", line 80, in new raise sp.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'mkdir -p CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out; python3 /home/bharat/opt/anaconda3/envs/py35/MetaCompass/bin/select_references.py tax CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.fasta CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out 1 2 1>> CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log 2>&1' returned non-zero exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/py35/lib/python3.5/site-packages/snakemake/executors.py", line 300, in _callback raise ex File "/home/bharat/opt/anaconda3/envs/py35/lib/python3.5/concurrent/futures/thread.py", line 55, in run result = self.fn(*self.args, **self.kwargs) File "/home/bharat/opt/anaconda3/envs/py35/lib/python3.5/site-packages/snakemake/executors.py", line 862, in run_wrapper show_traceback=True)) snakemake.exceptions.RuleException: CalledProcessError in line 82 of /home/bharat/opt/anaconda3/envs/py35/MetaCompass/snakemake/metacompass.iter0.paired.py: Command 'mkdir -p CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out; python3 /home/bharat/opt/anaconda3/envs/py35/MetaCompass/bin/select_references.py tax CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.fasta CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out 1 2 1>> CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log 2>&1' returned non-zero exit status 1 File "/home/bharat/opt/anaconda3/envs/py35/MetaCompass/snakemake/metacompass.iter0.paired.py", line 82, in __rule_reference_recruitment

RuleException: CalledProcessError in line 82 of /home/bharat/opt/anaconda3/envs/py35/MetaCompass/snakemake/metacompass.iter0.paired.py: Command 'mkdir -p CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out; python3 /home/bharat/opt/anaconda3/envs/py35/MetaCompass/bin/select_references.py tax CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.fasta CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out 1 2 1>> CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log 2>&1' returned non-zero exit status 1 File "/home/bharat/opt/anaconda3/envs/py35/MetaCompass/snakemake/metacompass.iter0.paired.py", line 82, in __rule_reference_recruitment File "/home/bharat/opt/anaconda3/envs/py35/lib/python3.5/concurrent/futures/thread.py", line 55, in run Removing output files of failed job reference_recruitment since they might be corrupted: CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out Releasing 1 _nodes (now 9223372036854775807). Releasing 1 _cores (now 1). Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message unlocking removing lock removing lock removed all locks ERROR: snakemake command failed; exiting.. touch: cannot touch 'CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out/run.fail': No such file or directory

vcepeda commented 5 years ago

Please share your CS1BS.output/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log, the error should be there.

bharat1912 commented 5 years ago

Thanks for the prompt response. Below is the information from CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log
File "/home/bharat/opt/anaconda3/envs/py35/MetaCompass/bin/select_references.py", line 282 else ^ SyntaxError: invalid syntax

bharat1912 commented 5 years ago

Just wandering if the python version will produce this error.

Here is the list and versions (built using anaconda3)

NAME: Anaconda3

VER: 2019.03

PLAT: linux-64

packages in environment at /home/bharat/opt/anaconda3/envs/metacompass:

#

Name Version Build Channel

_libgcc_mutex 0.1 main
asn1crypto 0.24.0 py36_0
bcrypt 3.1.6 py36h7b6447c_0
blas 1.0 mkl
blast 2.9.0 pl526h979a64d_3 bioconda bzip2 1.0.8 h7b6447c_0
ca-certificates 2019.5.15 0
certifi 2019.6.16 py36_0
cffi 1.12.3 py36h2e261b9_0
chardet 3.0.4 py36_1
cryptography 2.7 py36h1ba5d50_0
curl 7.65.2 hbc83047_0
docutils 0.14 py36_0
dropbox 9.3.0 py36_0
entrez-direct 11.0 pl526_0 bioconda expat 2.2.6 he6710b0_0
filechunkio 1.6 py36_0 bioconda ftputil 3.2 py36_0 bioconda idna 2.8 py36_0
intel-openmp 2019.4 243
krb5 1.16.1 h173b8e3_7
libcurl 7.65.2 h20c2e04_0
libdeflate 1.0 h14c3975_1 bioconda libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc 7.2.0 h69d50b8_2
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
libsodium 1.0.16 h1bed415_0
libssh2 1.8.2 h1ba5d50_0
libstdcxx-ng 9.1.0 hdf63c60_0
megahit 1.2.6 h8b12597_0 bioconda meryl 2013 0 bioconda mkl 2019.4 243
mkl_fft 1.0.12 py36ha843d7b_0
mkl_random 1.0.2 py36hd81dba3_0
ncurses 6.1 he6710b0_1
numpy 1.16.4 py36h7e9f1db_0
numpy-base 1.16.4 py36hde5b4d6_0
openjdk 8.0.152 h46b5887_1
openssl 1.1.1c h7b6447c_1
pandas 0.24.2 py36he6710b0_0
paramiko 2.4.2 py36_0
pcre 8.43 he6710b0_0
perl 5.26.2 h14c3975_0
perl-app-cpanminus 1.7044 pl526_1 bioconda perl-archive-tar 2.32 pl526_0 bioconda perl-base 2.23 pl526_1 bioconda perl-business-isbn 3.004 pl526_0 bioconda perl-business-isbn-data 20140910.003 pl526_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-compress-raw-bzip2 2.086 pl526hf484d3e_0 bioconda perl-compress-raw-zlib 2.086 pl526h6bb024c_1 bioconda perl-constant 1.33 pl526_1 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-digest-hmac 1.03 pl526_3 bioconda perl-digest-md5 2.55 pl526_0 bioconda perl-encode 2.88 pl526_1 bioconda perl-encode-locale 1.05 pl526_6 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-file-listing 6.04 pl526_1 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-html-parser 3.72 pl526h6bb024c_5 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-html-tree 5.07 pl526_1 bioconda perl-http-cookies 6.04 pl526_0 bioconda perl-http-daemon 6.01 pl526_1 bioconda perl-http-date 6.02 pl526_3 bioconda perl-http-message 6.18 pl526_0 bioconda perl-http-negotiate 6.01 pl526_3 bioconda perl-io-compress 2.086 pl526hf484d3e_0 bioconda perl-io-html 1.001 pl526_2 bioconda perl-io-socket-ssl 2.066 pl526_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-libwww-perl 6.39 pl526_0 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-lwp-mediatypes 6.04 pl526_0 bioconda perl-lwp-protocol-https 6.07 pl526_4 bioconda perl-mime-base64 3.15 pl526_1 bioconda perl-mozilla-ca 20180117 pl526_1 bioconda perl-net-http 6.19 pl526_0 bioconda perl-net-ssleay 1.88 pl526h90d6eec_0 bioconda perl-ntlm 1.09 pl526_4 bioconda perl-parent 0.236 pl526_1 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-scalar-list-utils 1.50 pl526h14c3975_0 bioconda perl-socket 2.027 pl526_1 bioconda perl-storable 3.15 pl526h14c3975_0 bioconda perl-test-requiresinternet 0.05 pl526_0 bioconda perl-time-local 1.28 pl526_1 bioconda perl-try-tiny 0.30 pl526_1 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-uri 1.76 pl526_0 bioconda perl-www-robotrules 6.02 pl526_3 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44 pl526h4e0c4b3_7 bioconda perl-xml-sax 1.02 pl526_0 bioconda perl-xml-sax-base 1.09 pl526_0 bioconda perl-xml-sax-expat 0.51 pl526_3 bioconda perl-xml-simple 2.25 pl526_1 bioconda perl-xsloader 0.24 pl526_0 bioconda pilon 1.23 0 bioconda pip 19.1.1 py36_0
psutil 5.6.3 py36h7b6447c_0
pyasn1 0.4.5 py_0
pycparser 2.19 py36_0
pynacl 1.3.0 py36h7b6447c_0
pyopenssl 19.0.0 py36_0
pysftp 0.2.9 py36_0 bioconda pysocks 1.7.0 py36_0
python 3.6.8 h0371630_0
python-dateutil 2.8.0 py36_0
pytz 2019.1 py_0
pyyaml 5.1.1 py36h7b6447c_0
readline 7.0 h7b6447c_5
requests 2.22.0 py36_0
samtools 1.9 h8571acd_11 bioconda setuptools 41.0.1 py36_0
six 1.12.0 py36_0
snakemake 3.13.3 py36_0 bioconda sqlite 3.29.0 h7b6447c_0
tk 8.6.8 hbc83047_0
urllib3 1.24.2 py36_0
wheel 0.33.4 py36_0
wrapt 1.11.2 py36h7b6447c_0
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zlib 1.2.11 h7b6447c_3

installed using active conda environment with metacompass from github

MetaCompass v1.3

Last updated: April 6th, 2019

vcepeda commented 5 years ago

I updated the code. Thanks!

bharat1912 commented 5 years ago

Thank you for updating the code.

  1. Updated $~/opt/anaconda3/envs/metacompass/MetaCompass$ git pull https://github.com/marbl/MetaCompass.git remote: Enumerating objects: 7, done. remote: Counting objects: 100% (7/7), done. remote: Compressing objects: 100% (4/4), done. remote: Total 4 (delta 3), reused 0 (delta 0), pack-reused 0 Unpacking objects: 100% (4/4), done. From https://github.com/marbl/MetaCompass

    • branch HEAD -> FETCH_HEAD Updating 3d187c6..7380e5e Fast-forward bin/select_references.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-)

  2. Ran the pipeline again but failed with a different error (metacompass) bharat@bharat-T3500:~/opt/anaconda3/envs/metacompass/MetaCompass$ python3 go_metacompass.py -P tutorial/CS1BS_ATBW8_GCCAAT_L001_R1.fastq,tutorial/CS1BS_ATBW8_GCCAAT_L001_R2.fastq -l 300 -o CS1BS.output_new -m 1 -t 4 checking for dependencies (Bowtie2, Blast, kmermask, Snakemake, etc) /home/bharat/opt/anaconda3/envs/metacompass/bin/snakemake Snakemake--->[OK] Bowtie2--->[OK] /home/bharat/opt/anaconda3/envs/metacompass/bin/blastn Blast+--->[OK] /home/bharat/opt/anaconda3/envs/metacompass/bin/kmer-mask kmer-mask--->[OK] /usr/bin/mash mash--->[OK] Provided cores: 4 Rules claiming more threads will be scaled down. Job counts: count jobs 1 all 1 assemble_unmapped 1 bam_sort 1 bowtie2_map 1 build_contigs 1 create_tsv 1 fastq2fasta 1 join_contigs 1 kmer_mask 1 merge_reads 1 pilon_contigs 1 pilon_map 1 reference_recruitment 1 sam_to_bam 14 Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807} Ready jobs (1): merge_reads Selected jobs (1): merge_reads Resources after job selection: {'_cores': 3, '_nodes': 9223372036854775806}

Job 11: ---merge fastq reads Reason: Missing output files: CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq

Releasing 1 _cores (now 4). Releasing 1 _nodes (now 9223372036854775807). Finished job 11. 1 of 14 steps (7%) done Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807} Ready jobs (1): kmer_mask Selected jobs (1): kmer_mask Resources after job selection: {'_cores': 0, '_nodes': 9223372036854775806}

Job 13: ---kmer-mask fastq Reason: Missing output files: CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.marker.match.1.fastq; Input files updated by another job: CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq

Releasing 4 _cores (now 4). Releasing 1 _nodes (now 9223372036854775807). Finished job 13. 2 of 14 steps (14%) done Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807} Ready jobs (1): fastq2fasta Selected jobs (1): fastq2fasta Resources after job selection: {'_cores': 3, '_nodes': 9223372036854775806}

Job 10: ---Converting fastq to fasta. Reason: Missing output files: CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.fasta; Input files updated by another job: CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.marker.match.1.fastq

Releasing 1 _cores (now 4). Releasing 1 _nodes (now 9223372036854775807). Finished job 10. 3 of 14 steps (21%) done Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807} Ready jobs (1): reference_recruitment Selected jobs (1): reference_recruitment Resources after job selection: {'_cores': 0, '_nodes': 9223372036854775806}

Job 6: ---reference recruitment. Reason: Missing output files: CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out/mc.refseq.fna; Input files updated by another job: CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.fasta, CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq

Full Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/metacompass/lib/python3.6/site-packages/snakemake/executors.py", line 923, in run_wrapper log, version, rule, conda_env, None) File "/home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/snakemake/metacompass.iter0.paired.py", line 170, in __rule_reference_recruitment bam = "%s.bam"%(rules.pilon_map.output.sam) File "/home/bharat/opt/anaconda3/envs/metacompass/lib/python3.6/site-packages/snakemake/shell.py", line 88, in new raise sp.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'mkdir -p CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out; python3 /home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/bin/select_references.py tax CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.fasta CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out 4 2 1>> CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log 2>&1' returned non-zero exit status 1.

Error in job reference_recruitment while creating output files CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out, CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out/mc.refseq.fna, CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out/mc.refseq.ids. Full Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/metacompass/lib/python3.6/site-packages/snakemake/executors.py", line 923, in run_wrapper log, version, rule, conda_env, None) File "/home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/snakemake/metacompass.iter0.paired.py", line 170, in __rule_reference_recruitment bam = "%s.bam"%(rules.pilon_map.output.sam) File "/home/bharat/opt/anaconda3/envs/metacompass/lib/python3.6/site-packages/snakemake/shell.py", line 88, in new raise sp.CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'mkdir -p CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out; python3 /home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/bin/select_references.py tax CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.fasta CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out 4 2 1>> CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log 2>&1' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/metacompass/lib/python3.6/site-packages/snakemake/executors.py", line 326, in _callback raise ex File "/home/bharat/opt/anaconda3/envs/metacompass/lib/python3.6/concurrent/futures/thread.py", line 56, in run result = self.fn(*self.args, **self.kwargs) File "/home/bharat/opt/anaconda3/envs/metacompass/lib/python3.6/site-packages/snakemake/executors.py", line 935, in run_wrapper show_traceback=True)) snakemake.exceptions.RuleException: CalledProcessError in line 82 of /home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/snakemake/metacompass.iter0.paired.py: Command 'mkdir -p CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out; python3 /home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/bin/select_references.py tax CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.fasta CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out 4 2 1>> CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log 2>&1' returned non-zero exit status 1. File "/home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/snakemake/metacompass.iter0.paired.py", line 82, in __rule_reference_recruitment

RuleException: CalledProcessError in line 82 of /home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/snakemake/metacompass.iter0.paired.py: Command 'mkdir -p CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out; python3 /home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/bin/select_references.py tax CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.fasta CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.merged.fq CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out 4 2 1>> CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log 2>&1' returned non-zero exit status 1. File "/home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/snakemake/metacompass.iter0.paired.py", line 82, in __rule_reference_recruitment File "/home/bharat/opt/anaconda3/envs/metacompass/lib/python3.6/concurrent/futures/thread.py", line 56, in run Removing output files of failed job reference_recruitment since they might be corrupted: CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out Releasing 4 _cores (now 4). Releasing 1 _nodes (now 9223372036854775807). Will exit after finishing currently running jobs. Exiting because a job execution failed. Look above for error message unlocking removing lock removing lock removed all locks ERROR: snakemake command failed; exiting.. touch: cannot touch 'CS1BS.output_new/CS1BS_ATBW8_GCCAAT_L001_R1.0.assembly.out/run.fail': No such file or directory

  1. The error is reported below from the CS1BS_ATBW8_GCCAAT_L001_R1.0.reference_recruitement.log is given below: Traceback (most recent call last): File "/home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/bin/select_references.py", line 432, in main() File "/home/bharat/opt/anaconda3/envs/metacompass/MetaCompass/bin/select_references.py", line 281, in main cutoff = sys.argv[7] IndexError: list index out of range
vcepeda commented 5 years ago

Now should be fixed. Please try again!