Job ID = 5720148 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T12:13:30 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 ) 2020-04-15T12:13:30 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 ) 2020-04-15T12:19:14 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 ) 2020-04-15T12:19:14 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 ) 2020-04-15T12:19:14 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 : 26,012,368 reads read : 52,024,736 reads written : 26,012,368 reads 0-length : 26,012,368 spots read : 20,055,199 reads read : 40,110,398 reads written : 20,055,199 reads 0-length : 20,055,199 spots read : 40,961,267 reads read : 81,922,534 reads written : 40,961,267 reads 0-length : 40,961,267 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: 00:00:01 Multiseed full-index search: 00:18:15 87028834 reads; of these: 87028834 (100.00%) were unpaired; of these: 35763222 (41.09%) aligned 0 times 38372290 (44.09%) aligned exactly 1 time 12893322 (14.82%) aligned >1 times 58.91% overall alignment rate Time searching: 00:18:16 Overall time: 00:18:16 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 24 files... [bam_rmdupse_core] 23642632 / 51265612 = 0.4612 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 22:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.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 22:17:09: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:17:09: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:17:16: 1000000 INFO @ Wed, 15 Apr 2020 22:17:23: 2000000 INFO @ Wed, 15 Apr 2020 22:17:29: 3000000 INFO @ Wed, 15 Apr 2020 22:17:36: 4000000 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 22:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.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 22:17:38: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:17:38: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:17:44: 5000000 INFO @ Wed, 15 Apr 2020 22:17:46: 1000000 INFO @ Wed, 15 Apr 2020 22:17:51: 6000000 INFO @ Wed, 15 Apr 2020 22:17:54: 2000000 INFO @ Wed, 15 Apr 2020 22:17:59: 7000000 INFO @ Wed, 15 Apr 2020 22:18:02: 3000000 INFO @ Wed, 15 Apr 2020 22:18:06: 8000000 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 22:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.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 22:18:08: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:18:08: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:18:10: 4000000 INFO @ Wed, 15 Apr 2020 22:18:14: 9000000 INFO @ Wed, 15 Apr 2020 22:18:17: 1000000 INFO @ Wed, 15 Apr 2020 22:18:18: 5000000 INFO @ Wed, 15 Apr 2020 22:18:22: 10000000 INFO @ Wed, 15 Apr 2020 22:18:25: 2000000 INFO @ Wed, 15 Apr 2020 22:18:26: 6000000 INFO @ Wed, 15 Apr 2020 22:18:30: 11000000 INFO @ Wed, 15 Apr 2020 22:18:33: 3000000 INFO @ Wed, 15 Apr 2020 22:18:34: 7000000 INFO @ Wed, 15 Apr 2020 22:18:38: 12000000 INFO @ Wed, 15 Apr 2020 22:18:41: 4000000 INFO @ Wed, 15 Apr 2020 22:18:42: 8000000 INFO @ Wed, 15 Apr 2020 22:18:47: 13000000 INFO @ Wed, 15 Apr 2020 22:18:49: 5000000 INFO @ Wed, 15 Apr 2020 22:18:50: 9000000 INFO @ Wed, 15 Apr 2020 22:18:55: 14000000 INFO @ Wed, 15 Apr 2020 22:18:57: 6000000 INFO @ Wed, 15 Apr 2020 22:18:58: 10000000 INFO @ Wed, 15 Apr 2020 22:19:03: 15000000 INFO @ Wed, 15 Apr 2020 22:19:05: 7000000 INFO @ Wed, 15 Apr 2020 22:19:06: 11000000 INFO @ Wed, 15 Apr 2020 22:19:10: 16000000 INFO @ Wed, 15 Apr 2020 22:19:13: 8000000 INFO @ Wed, 15 Apr 2020 22:19:14: 12000000 INFO @ Wed, 15 Apr 2020 22:19:18: 17000000 INFO @ Wed, 15 Apr 2020 22:19:21: 9000000 INFO @ Wed, 15 Apr 2020 22:19:22: 13000000 INFO @ Wed, 15 Apr 2020 22:19:26: 18000000 INFO @ Wed, 15 Apr 2020 22:19:29: 10000000 INFO @ Wed, 15 Apr 2020 22:19:30: 14000000 INFO @ Wed, 15 Apr 2020 22:19:34: 19000000 INFO @ Wed, 15 Apr 2020 22:19:37: 11000000 INFO @ Wed, 15 Apr 2020 22:19:38: 15000000 INFO @ Wed, 15 Apr 2020 22:19:42: 20000000 INFO @ Wed, 15 Apr 2020 22:19:45: 12000000 INFO @ Wed, 15 Apr 2020 22:19:46: 16000000 INFO @ Wed, 15 Apr 2020 22:19:50: 21000000 INFO @ Wed, 15 Apr 2020 22:19:53: 13000000 INFO @ Wed, 15 Apr 2020 22:19:54: 17000000 INFO @ Wed, 15 Apr 2020 22:19:59: 22000000 INFO @ Wed, 15 Apr 2020 22:20:00: 14000000 INFO @ Wed, 15 Apr 2020 22:20:02: 18000000 INFO @ Wed, 15 Apr 2020 22:20:08: 23000000 INFO @ Wed, 15 Apr 2020 22:20:08: 15000000 INFO @ Wed, 15 Apr 2020 22:20:10: 19000000 INFO @ Wed, 15 Apr 2020 22:20:16: 16000000 INFO @ Wed, 15 Apr 2020 22:20:16: 24000000 INFO @ Wed, 15 Apr 2020 22:20:18: 20000000 INFO @ Wed, 15 Apr 2020 22:20:23: 17000000 INFO @ Wed, 15 Apr 2020 22:20:24: 25000000 INFO @ Wed, 15 Apr 2020 22:20:26: 21000000 INFO @ Wed, 15 Apr 2020 22:20:31: 18000000 INFO @ Wed, 15 Apr 2020 22:20:32: 26000000 INFO @ Wed, 15 Apr 2020 22:20:34: 22000000 INFO @ Wed, 15 Apr 2020 22:20:39: 19000000 INFO @ Wed, 15 Apr 2020 22:20:40: 27000000 INFO @ Wed, 15 Apr 2020 22:20:41: 23000000 INFO @ Wed, 15 Apr 2020 22:20:45: #1 tag size is determined as 55 bps INFO @ Wed, 15 Apr 2020 22:20:45: #1 tag size = 55 INFO @ Wed, 15 Apr 2020 22:20:45: #1 total tags in treatment: 27622980 INFO @ Wed, 15 Apr 2020 22:20:45: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:20:45: #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 22:20:45: #1 tags after filtering in treatment: 27622980 INFO @ Wed, 15 Apr 2020 22:20:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:20:45: #1 finished! INFO @ Wed, 15 Apr 2020 22:20:45: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:20:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:20:47: 20000000 INFO @ Wed, 15 Apr 2020 22:20:47: #2 number of paired peaks: 216 WARNING @ Wed, 15 Apr 2020 22:20:47: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Wed, 15 Apr 2020 22:20:47: start model_add_line... INFO @ Wed, 15 Apr 2020 22:20:47: start X-correlation... INFO @ Wed, 15 Apr 2020 22:20:47: end of X-cor INFO @ Wed, 15 Apr 2020 22:20:47: #2 finished! INFO @ Wed, 15 Apr 2020 22:20:47: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:20:47: #2 alternative fragment length(s) may be 1,19,47,538,554 bps INFO @ Wed, 15 Apr 2020 22:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.05_model.r WARNING @ Wed, 15 Apr 2020 22:20:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:20:47: #2 You may need to consider one of the other alternative d(s): 1,19,47,538,554 WARNING @ Wed, 15 Apr 2020 22:20:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:20:47: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:20:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:20:49: 24000000 INFO @ Wed, 15 Apr 2020 22:20:54: 21000000 INFO @ Wed, 15 Apr 2020 22:20:57: 25000000 INFO @ Wed, 15 Apr 2020 22:21:02: 22000000 INFO @ Wed, 15 Apr 2020 22:21:05: 26000000 INFO @ Wed, 15 Apr 2020 22:21:10: 23000000 INFO @ Wed, 15 Apr 2020 22:21:12: 27000000 INFO @ Wed, 15 Apr 2020 22:21:17: #1 tag size is determined as 55 bps INFO @ Wed, 15 Apr 2020 22:21:17: #1 tag size = 55 INFO @ Wed, 15 Apr 2020 22:21:17: #1 total tags in treatment: 27622980 INFO @ Wed, 15 Apr 2020 22:21:17: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:21:17: #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 22:21:18: #1 tags after filtering in treatment: 27622980 INFO @ Wed, 15 Apr 2020 22:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:21:18: #1 finished! INFO @ Wed, 15 Apr 2020 22:21:18: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:21:18: 24000000 INFO @ Wed, 15 Apr 2020 22:21:19: #2 number of paired peaks: 216 WARNING @ Wed, 15 Apr 2020 22:21:19: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Wed, 15 Apr 2020 22:21:19: start model_add_line... INFO @ Wed, 15 Apr 2020 22:21:20: start X-correlation... INFO @ Wed, 15 Apr 2020 22:21:20: end of X-cor INFO @ Wed, 15 Apr 2020 22:21:20: #2 finished! INFO @ Wed, 15 Apr 2020 22:21:20: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:21:20: #2 alternative fragment length(s) may be 1,19,47,538,554 bps INFO @ Wed, 15 Apr 2020 22:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.10_model.r WARNING @ Wed, 15 Apr 2020 22:21:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:21:20: #2 You may need to consider one of the other alternative d(s): 1,19,47,538,554 WARNING @ Wed, 15 Apr 2020 22:21:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:21:20: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:21:25: 25000000 INFO @ Wed, 15 Apr 2020 22:21:26: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:21:32: 26000000 INFO @ Wed, 15 Apr 2020 22:21:39: 27000000 INFO @ Wed, 15 Apr 2020 22:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.05_summits.bed INFO @ Wed, 15 Apr 2020 22:21:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:21:44: #1 tag size is determined as 55 bps INFO @ Wed, 15 Apr 2020 22:21:44: #1 tag size = 55 INFO @ Wed, 15 Apr 2020 22:21:44: #1 total tags in treatment: 27622980 INFO @ Wed, 15 Apr 2020 22:21:44: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:21:44: #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 22:21:44: #1 tags after filtering in treatment: 27622980 INFO @ Wed, 15 Apr 2020 22:21:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:21:44: #1 finished! INFO @ Wed, 15 Apr 2020 22:21:44: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:21:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:21:46: #2 number of paired peaks: 216 WARNING @ Wed, 15 Apr 2020 22:21:46: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Wed, 15 Apr 2020 22:21:46: start model_add_line... INFO @ Wed, 15 Apr 2020 22:21:46: start X-correlation... INFO @ Wed, 15 Apr 2020 22:21:46: end of X-cor INFO @ Wed, 15 Apr 2020 22:21:46: #2 finished! INFO @ Wed, 15 Apr 2020 22:21:46: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:21:46: #2 alternative fragment length(s) may be 1,19,47,538,554 bps INFO @ Wed, 15 Apr 2020 22:21:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.20_model.r WARNING @ Wed, 15 Apr 2020 22:21:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:21:46: #2 You may need to consider one of the other alternative d(s): 1,19,47,538,554 WARNING @ Wed, 15 Apr 2020 22:21:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:21:46: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:21:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:21:59: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:22:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:22:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.10_summits.bed INFO @ Wed, 15 Apr 2020 22:22:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:22:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 15 Apr 2020 22:22:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:22:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:22:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702591/SRX5702591.20_summits.bed INFO @ Wed, 15 Apr 2020 22:22:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。