Job ID = 5720145 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,389,429 reads read : 74,778,858 reads written : 37,389,429 reads 0-length : 37,389,429 2020-04-15T12:27:32 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 ) 2020-04-15T12:29:29 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 : 22,817,177 reads read : 45,634,354 reads written : 22,817,177 reads 0-length : 22,817,177 2020-04-15T13:04:13 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 ) 2020-04-15T13:05:33 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 : 105,354,363 reads read : 210,708,726 reads written : 105,354,363 reads 0-length : 105,354,363 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: 00:31:21 165560969 reads; of these: 165560969 (100.00%) were unpaired; of these: 85618399 (51.71%) aligned 0 times 56336742 (34.03%) aligned exactly 1 time 23605828 (14.26%) aligned >1 times 48.29% overall alignment rate Time searching: 00:31:21 Overall time: 00:31:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 36 files... [bam_rmdupse_core] 36052233 / 79942570 = 0.4510 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, 15 Apr 2020 23:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.bam'] # control file = None # effective genome size = 9.00e+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, 15 Apr 2020 23:10:55: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:10:55: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:11:00: 1000000 INFO @ Wed, 15 Apr 2020 23:11:05: 2000000 INFO @ Wed, 15 Apr 2020 23:11:09: 3000000 INFO @ Wed, 15 Apr 2020 23:11:14: 4000000 INFO @ Wed, 15 Apr 2020 23:11:19: 5000000 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, 15 Apr 2020 23:11:24: 6000000 INFO @ Wed, 15 Apr 2020 23:11:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.bam'] # control file = None # effective genome size = 9.00e+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, 15 Apr 2020 23:11:25: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:11:25: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:11:28: 7000000 INFO @ Wed, 15 Apr 2020 23:11:30: 1000000 INFO @ Wed, 15 Apr 2020 23:11:33: 8000000 INFO @ Wed, 15 Apr 2020 23:11:35: 2000000 INFO @ Wed, 15 Apr 2020 23:11:38: 9000000 INFO @ Wed, 15 Apr 2020 23:11:40: 3000000 INFO @ Wed, 15 Apr 2020 23:11:43: 10000000 INFO @ Wed, 15 Apr 2020 23:11:45: 4000000 INFO @ Wed, 15 Apr 2020 23:11:48: 11000000 INFO @ Wed, 15 Apr 2020 23:11:50: 5000000 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, 15 Apr 2020 23:11:53: 12000000 INFO @ Wed, 15 Apr 2020 23:11:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.bam'] # control file = None # effective genome size = 9.00e+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, 15 Apr 2020 23:11:55: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:11:55: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:11:55: 6000000 INFO @ Wed, 15 Apr 2020 23:11:58: 13000000 INFO @ Wed, 15 Apr 2020 23:12:00: 1000000 INFO @ Wed, 15 Apr 2020 23:12:00: 7000000 INFO @ Wed, 15 Apr 2020 23:12:03: 14000000 INFO @ Wed, 15 Apr 2020 23:12:05: 2000000 INFO @ Wed, 15 Apr 2020 23:12:05: 8000000 INFO @ Wed, 15 Apr 2020 23:12:08: 15000000 INFO @ Wed, 15 Apr 2020 23:12:10: 9000000 INFO @ Wed, 15 Apr 2020 23:12:10: 3000000 INFO @ Wed, 15 Apr 2020 23:12:13: 16000000 INFO @ Wed, 15 Apr 2020 23:12:15: 10000000 INFO @ Wed, 15 Apr 2020 23:12:15: 4000000 INFO @ Wed, 15 Apr 2020 23:12:18: 17000000 INFO @ Wed, 15 Apr 2020 23:12:20: 11000000 INFO @ Wed, 15 Apr 2020 23:12:20: 5000000 INFO @ Wed, 15 Apr 2020 23:12:23: 18000000 INFO @ Wed, 15 Apr 2020 23:12:25: 6000000 INFO @ Wed, 15 Apr 2020 23:12:25: 12000000 INFO @ Wed, 15 Apr 2020 23:12:28: 19000000 INFO @ Wed, 15 Apr 2020 23:12:30: 7000000 INFO @ Wed, 15 Apr 2020 23:12:30: 13000000 INFO @ Wed, 15 Apr 2020 23:12:33: 20000000 INFO @ Wed, 15 Apr 2020 23:12:35: 8000000 INFO @ Wed, 15 Apr 2020 23:12:35: 14000000 INFO @ Wed, 15 Apr 2020 23:12:38: 21000000 INFO @ Wed, 15 Apr 2020 23:12:40: 9000000 INFO @ Wed, 15 Apr 2020 23:12:40: 15000000 INFO @ Wed, 15 Apr 2020 23:12:43: 22000000 INFO @ Wed, 15 Apr 2020 23:12:45: 10000000 INFO @ Wed, 15 Apr 2020 23:12:45: 16000000 INFO @ Wed, 15 Apr 2020 23:12:48: 23000000 INFO @ Wed, 15 Apr 2020 23:12:50: 11000000 INFO @ Wed, 15 Apr 2020 23:12:50: 17000000 INFO @ Wed, 15 Apr 2020 23:12:53: 24000000 INFO @ Wed, 15 Apr 2020 23:12:55: 12000000 INFO @ Wed, 15 Apr 2020 23:12:55: 18000000 INFO @ Wed, 15 Apr 2020 23:12:58: 25000000 INFO @ Wed, 15 Apr 2020 23:13:00: 13000000 INFO @ Wed, 15 Apr 2020 23:13:00: 19000000 INFO @ Wed, 15 Apr 2020 23:13:03: 26000000 INFO @ Wed, 15 Apr 2020 23:13:05: 14000000 INFO @ Wed, 15 Apr 2020 23:13:05: 20000000 INFO @ Wed, 15 Apr 2020 23:13:08: 27000000 INFO @ Wed, 15 Apr 2020 23:13:09: 15000000 INFO @ Wed, 15 Apr 2020 23:13:10: 21000000 INFO @ Wed, 15 Apr 2020 23:13:13: 28000000 INFO @ Wed, 15 Apr 2020 23:13:14: 16000000 INFO @ Wed, 15 Apr 2020 23:13:15: 22000000 INFO @ Wed, 15 Apr 2020 23:13:18: 29000000 INFO @ Wed, 15 Apr 2020 23:13:19: 17000000 INFO @ Wed, 15 Apr 2020 23:13:20: 23000000 INFO @ Wed, 15 Apr 2020 23:13:23: 30000000 INFO @ Wed, 15 Apr 2020 23:13:24: 18000000 INFO @ Wed, 15 Apr 2020 23:13:25: 24000000 INFO @ Wed, 15 Apr 2020 23:13:28: 31000000 INFO @ Wed, 15 Apr 2020 23:13:29: 19000000 INFO @ Wed, 15 Apr 2020 23:13:30: 25000000 INFO @ Wed, 15 Apr 2020 23:13:33: 32000000 INFO @ Wed, 15 Apr 2020 23:13:34: 20000000 INFO @ Wed, 15 Apr 2020 23:13:35: 26000000 INFO @ Wed, 15 Apr 2020 23:13:38: 33000000 INFO @ Wed, 15 Apr 2020 23:13:39: 21000000 INFO @ Wed, 15 Apr 2020 23:13:40: 27000000 INFO @ Wed, 15 Apr 2020 23:13:43: 34000000 INFO @ Wed, 15 Apr 2020 23:13:44: 22000000 INFO @ Wed, 15 Apr 2020 23:13:45: 28000000 INFO @ Wed, 15 Apr 2020 23:13:48: 35000000 INFO @ Wed, 15 Apr 2020 23:13:49: 23000000 INFO @ Wed, 15 Apr 2020 23:13:50: 29000000 INFO @ Wed, 15 Apr 2020 23:13:53: 36000000 INFO @ Wed, 15 Apr 2020 23:13:54: 24000000 INFO @ Wed, 15 Apr 2020 23:13:55: 30000000 INFO @ Wed, 15 Apr 2020 23:13:58: 37000000 INFO @ Wed, 15 Apr 2020 23:13:59: 25000000 INFO @ Wed, 15 Apr 2020 23:14:00: 31000000 INFO @ Wed, 15 Apr 2020 23:14:03: 38000000 INFO @ Wed, 15 Apr 2020 23:14:04: 26000000 INFO @ Wed, 15 Apr 2020 23:14:05: 32000000 INFO @ Wed, 15 Apr 2020 23:14:08: 39000000 INFO @ Wed, 15 Apr 2020 23:14:09: 27000000 INFO @ Wed, 15 Apr 2020 23:14:10: 33000000 INFO @ Wed, 15 Apr 2020 23:14:13: 40000000 INFO @ Wed, 15 Apr 2020 23:14:14: 28000000 INFO @ Wed, 15 Apr 2020 23:14:15: 34000000 INFO @ Wed, 15 Apr 2020 23:14:18: 41000000 INFO @ Wed, 15 Apr 2020 23:14:19: 29000000 INFO @ Wed, 15 Apr 2020 23:14:20: 35000000 INFO @ Wed, 15 Apr 2020 23:14:23: 42000000 INFO @ Wed, 15 Apr 2020 23:14:24: 30000000 INFO @ Wed, 15 Apr 2020 23:14:25: 36000000 INFO @ Wed, 15 Apr 2020 23:14:28: 43000000 INFO @ Wed, 15 Apr 2020 23:14:29: 31000000 INFO @ Wed, 15 Apr 2020 23:14:30: 37000000 INFO @ Wed, 15 Apr 2020 23:14:33: #1 tag size is determined as 52 bps INFO @ Wed, 15 Apr 2020 23:14:33: #1 tag size = 52 INFO @ Wed, 15 Apr 2020 23:14:33: #1 total tags in treatment: 43890337 INFO @ Wed, 15 Apr 2020 23:14:33: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:14:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:14:34: #1 tags after filtering in treatment: 43890337 INFO @ Wed, 15 Apr 2020 23:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:14:34: #1 finished! INFO @ Wed, 15 Apr 2020 23:14:34: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:14:34: 32000000 INFO @ Wed, 15 Apr 2020 23:14:34: 38000000 INFO @ Wed, 15 Apr 2020 23:14:36: #2 number of paired peaks: 0 WARNING @ Wed, 15 Apr 2020 23:14:36: 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, 15 Apr 2020 23:14:36: Process for pairing-model is terminated! INFO @ Wed, 15 Apr 2020 23:14:39: 33000000 INFO @ Wed, 15 Apr 2020 23:14:39: 39000000 cut: /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.05_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/ce10/SRX5702588/SRX5702588.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:14:44: 34000000 INFO @ Wed, 15 Apr 2020 23:14:44: 40000000 INFO @ Wed, 15 Apr 2020 23:14:49: 35000000 INFO @ Wed, 15 Apr 2020 23:14:49: 41000000 INFO @ Wed, 15 Apr 2020 23:14:54: 36000000 INFO @ Wed, 15 Apr 2020 23:14:55: 42000000 INFO @ Wed, 15 Apr 2020 23:14:58: 37000000 INFO @ Wed, 15 Apr 2020 23:15:00: 43000000 INFO @ Wed, 15 Apr 2020 23:15:03: 38000000 INFO @ Wed, 15 Apr 2020 23:15:05: #1 tag size is determined as 52 bps INFO @ Wed, 15 Apr 2020 23:15:05: #1 tag size = 52 INFO @ Wed, 15 Apr 2020 23:15:05: #1 total tags in treatment: 43890337 INFO @ Wed, 15 Apr 2020 23:15:05: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:15:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:15:05: #1 tags after filtering in treatment: 43890337 INFO @ Wed, 15 Apr 2020 23:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:15:05: #1 finished! INFO @ Wed, 15 Apr 2020 23:15:05: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:15:08: #2 number of paired peaks: 0 WARNING @ Wed, 15 Apr 2020 23:15:08: 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, 15 Apr 2020 23:15:08: Process for pairing-model is terminated! INFO @ Wed, 15 Apr 2020 23:15:08: 39000000 cut: /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.10_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/ce10/SRX5702588/SRX5702588.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:15:13: 40000000 INFO @ Wed, 15 Apr 2020 23:15:18: 41000000 INFO @ Wed, 15 Apr 2020 23:15:23: 42000000 INFO @ Wed, 15 Apr 2020 23:15:28: 43000000 INFO @ Wed, 15 Apr 2020 23:15:32: #1 tag size is determined as 52 bps INFO @ Wed, 15 Apr 2020 23:15:32: #1 tag size = 52 INFO @ Wed, 15 Apr 2020 23:15:32: #1 total tags in treatment: 43890337 INFO @ Wed, 15 Apr 2020 23:15:32: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:15:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:15:33: #1 tags after filtering in treatment: 43890337 INFO @ Wed, 15 Apr 2020 23:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:15:33: #1 finished! INFO @ Wed, 15 Apr 2020 23:15:33: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:15:36: #2 number of paired peaks: 0 WARNING @ Wed, 15 Apr 2020 23:15:36: 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, 15 Apr 2020 23:15:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.20_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/ce10/SRX5702588/SRX5702588.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX5702588/SRX5702588.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。