Job ID = 5791675 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:21:28 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:21:48 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:21:48 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:21:48 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:23:21 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:32:05 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:37:02 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:40:56 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-22T01:50:28 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 17,096,369 reads read : 34,192,738 reads written : 34,192,738 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:34 17096369 reads; of these: 17096369 (100.00%) were paired; of these: 7068491 (41.34%) aligned concordantly 0 times 8289507 (48.49%) aligned concordantly exactly 1 time 1738371 (10.17%) aligned concordantly >1 times ---- 7068491 pairs aligned concordantly 0 times; of these: 1763874 (24.95%) aligned discordantly 1 time ---- 5304617 pairs aligned 0 times concordantly or discordantly; of these: 10609234 mates make up the pairs; of these: 9371067 (88.33%) aligned 0 times 364325 (3.43%) aligned exactly 1 time 873842 (8.24%) aligned >1 times 72.59% overall alignment rate Time searching: 00:17:34 Overall time: 00:17:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1799799 / 11713410 = 0.1537 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 11:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 11:23:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:23:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:24:07: 1000000 INFO @ Wed, 22 Apr 2020 11:24:15: 2000000 INFO @ Wed, 22 Apr 2020 11:24:23: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 11:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 11:24:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:24:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:24:31: 4000000 INFO @ Wed, 22 Apr 2020 11:24:38: 1000000 INFO @ Wed, 22 Apr 2020 11:24:41: 5000000 INFO @ Wed, 22 Apr 2020 11:24:48: 2000000 INFO @ Wed, 22 Apr 2020 11:24:50: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 11:24:58: 3000000 INFO @ Wed, 22 Apr 2020 11:24:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 11:24:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:24:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:25:00: 7000000 INFO @ Wed, 22 Apr 2020 11:25:08: 4000000 INFO @ Wed, 22 Apr 2020 11:25:09: 1000000 INFO @ Wed, 22 Apr 2020 11:25:10: 8000000 INFO @ Wed, 22 Apr 2020 11:25:18: 5000000 INFO @ Wed, 22 Apr 2020 11:25:19: 2000000 INFO @ Wed, 22 Apr 2020 11:25:20: 9000000 INFO @ Wed, 22 Apr 2020 11:25:28: 6000000 INFO @ Wed, 22 Apr 2020 11:25:28: 3000000 INFO @ Wed, 22 Apr 2020 11:25:30: 10000000 INFO @ Wed, 22 Apr 2020 11:25:38: 7000000 INFO @ Wed, 22 Apr 2020 11:25:38: 4000000 INFO @ Wed, 22 Apr 2020 11:25:40: 11000000 INFO @ Wed, 22 Apr 2020 11:25:48: 8000000 INFO @ Wed, 22 Apr 2020 11:25:48: 5000000 INFO @ Wed, 22 Apr 2020 11:25:50: 12000000 INFO @ Wed, 22 Apr 2020 11:25:58: 9000000 INFO @ Wed, 22 Apr 2020 11:25:58: 6000000 INFO @ Wed, 22 Apr 2020 11:26:00: 13000000 INFO @ Wed, 22 Apr 2020 11:26:08: 10000000 INFO @ Wed, 22 Apr 2020 11:26:08: 7000000 INFO @ Wed, 22 Apr 2020 11:26:10: 14000000 INFO @ Wed, 22 Apr 2020 11:26:17: 11000000 INFO @ Wed, 22 Apr 2020 11:26:18: 8000000 INFO @ Wed, 22 Apr 2020 11:26:19: 15000000 INFO @ Wed, 22 Apr 2020 11:26:27: 12000000 INFO @ Wed, 22 Apr 2020 11:26:28: 9000000 INFO @ Wed, 22 Apr 2020 11:26:29: 16000000 INFO @ Wed, 22 Apr 2020 11:26:37: 13000000 INFO @ Wed, 22 Apr 2020 11:26:38: 10000000 INFO @ Wed, 22 Apr 2020 11:26:39: 17000000 INFO @ Wed, 22 Apr 2020 11:26:47: 14000000 INFO @ Wed, 22 Apr 2020 11:26:47: 11000000 INFO @ Wed, 22 Apr 2020 11:26:49: 18000000 INFO @ Wed, 22 Apr 2020 11:26:57: 15000000 INFO @ Wed, 22 Apr 2020 11:26:57: 12000000 INFO @ Wed, 22 Apr 2020 11:26:59: 19000000 INFO @ Wed, 22 Apr 2020 11:27:07: 16000000 INFO @ Wed, 22 Apr 2020 11:27:07: 13000000 INFO @ Wed, 22 Apr 2020 11:27:09: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:27:17: 17000000 INFO @ Wed, 22 Apr 2020 11:27:17: 14000000 INFO @ Wed, 22 Apr 2020 11:27:19: 21000000 INFO @ Wed, 22 Apr 2020 11:27:21: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:27:21: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:27:21: #1 total tags in treatment: 8426750 INFO @ Wed, 22 Apr 2020 11:27:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:27:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:27:21: #1 tags after filtering in treatment: 6338612 INFO @ Wed, 22 Apr 2020 11:27:21: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 11:27:21: #1 finished! INFO @ Wed, 22 Apr 2020 11:27:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:27:22: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:27:22: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 11:27:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:27:26: 18000000 INFO @ Wed, 22 Apr 2020 11:27:27: 15000000 INFO @ Wed, 22 Apr 2020 11:27:36: 19000000 INFO @ Wed, 22 Apr 2020 11:27:36: 16000000 INFO @ Wed, 22 Apr 2020 11:27:46: 20000000 INFO @ Wed, 22 Apr 2020 11:27:46: 17000000 INFO @ Wed, 22 Apr 2020 11:27:56: 21000000 INFO @ Wed, 22 Apr 2020 11:27:56: 18000000 INFO @ Wed, 22 Apr 2020 11:27:58: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:27:58: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:27:58: #1 total tags in treatment: 8426750 INFO @ Wed, 22 Apr 2020 11:27:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:27:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:27:58: #1 tags after filtering in treatment: 6338612 INFO @ Wed, 22 Apr 2020 11:27:58: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 11:27:58: #1 finished! INFO @ Wed, 22 Apr 2020 11:27:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:27:58: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:27:58: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 11:27:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:28:05: 19000000 INFO @ Wed, 22 Apr 2020 11:28:14: 20000000 INFO @ Wed, 22 Apr 2020 11:28:22: 21000000 INFO @ Wed, 22 Apr 2020 11:28:24: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:28:24: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:28:24: #1 total tags in treatment: 8426750 INFO @ Wed, 22 Apr 2020 11:28:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:28:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:28:24: #1 tags after filtering in treatment: 6338612 INFO @ Wed, 22 Apr 2020 11:28:24: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 11:28:24: #1 finished! INFO @ Wed, 22 Apr 2020 11:28:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:28:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:28:25: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:28:25: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 11:28:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409635/SRX7409635.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling