Job ID = 6497474 SRX = SRX494975 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:34:49 prefetch.2.10.7: 1) Downloading 'SRR1198507'... 2020-06-25T22:34:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:38:03 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:38:03 prefetch.2.10.7: 1) 'SRR1198507' was downloaded successfully Read 33231749 spots for SRR1198507/SRR1198507.sra Written 33231749 spots for SRR1198507/SRR1198507.sra 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: 00:06:20 33231749 reads; of these: 33231749 (100.00%) were unpaired; of these: 359438 (1.08%) aligned 0 times 27444412 (82.58%) aligned exactly 1 time 5427899 (16.33%) aligned >1 times 98.92% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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 12 files... [bam_rmdupse_core] 7401799 / 32872311 = 0.2252 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 @ Fri, 26 Jun 2020 07:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.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 @ Fri, 26 Jun 2020 07:52:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:26: 1000000 INFO @ Fri, 26 Jun 2020 07:52:32: 2000000 INFO @ Fri, 26 Jun 2020 07:52:39: 3000000 INFO @ Fri, 26 Jun 2020 07:52:45: 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 @ Fri, 26 Jun 2020 07:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.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 @ Fri, 26 Jun 2020 07:52:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:51: 5000000 INFO @ Fri, 26 Jun 2020 07:52:57: 1000000 INFO @ Fri, 26 Jun 2020 07:52:57: 6000000 INFO @ Fri, 26 Jun 2020 07:53:04: 2000000 INFO @ Fri, 26 Jun 2020 07:53:04: 7000000 INFO @ Fri, 26 Jun 2020 07:53:11: 8000000 INFO @ Fri, 26 Jun 2020 07:53:11: 3000000 INFO @ Fri, 26 Jun 2020 07:53:17: 9000000 INFO @ Fri, 26 Jun 2020 07:53:18: 4000000 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 @ Fri, 26 Jun 2020 07:53:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.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 @ Fri, 26 Jun 2020 07:53:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:53:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:53:24: 10000000 INFO @ Fri, 26 Jun 2020 07:53:25: 5000000 INFO @ Fri, 26 Jun 2020 07:53:28: 1000000 INFO @ Fri, 26 Jun 2020 07:53:31: 11000000 INFO @ Fri, 26 Jun 2020 07:53:32: 6000000 INFO @ Fri, 26 Jun 2020 07:53:35: 2000000 INFO @ Fri, 26 Jun 2020 07:53:37: 12000000 INFO @ Fri, 26 Jun 2020 07:53:40: 7000000 INFO @ Fri, 26 Jun 2020 07:53:43: 3000000 INFO @ Fri, 26 Jun 2020 07:53:44: 13000000 INFO @ Fri, 26 Jun 2020 07:53:47: 8000000 INFO @ Fri, 26 Jun 2020 07:53:50: 4000000 INFO @ Fri, 26 Jun 2020 07:53:51: 14000000 INFO @ Fri, 26 Jun 2020 07:53:55: 9000000 INFO @ Fri, 26 Jun 2020 07:53:57: 15000000 INFO @ Fri, 26 Jun 2020 07:53:58: 5000000 INFO @ Fri, 26 Jun 2020 07:54:03: 10000000 INFO @ Fri, 26 Jun 2020 07:54:04: 16000000 INFO @ Fri, 26 Jun 2020 07:54:06: 6000000 INFO @ Fri, 26 Jun 2020 07:54:10: 11000000 INFO @ Fri, 26 Jun 2020 07:54:11: 17000000 INFO @ Fri, 26 Jun 2020 07:54:13: 7000000 INFO @ Fri, 26 Jun 2020 07:54:17: 18000000 INFO @ Fri, 26 Jun 2020 07:54:18: 12000000 INFO @ Fri, 26 Jun 2020 07:54:21: 8000000 INFO @ Fri, 26 Jun 2020 07:54:24: 19000000 INFO @ Fri, 26 Jun 2020 07:54:25: 13000000 INFO @ Fri, 26 Jun 2020 07:54:28: 9000000 INFO @ Fri, 26 Jun 2020 07:54:31: 20000000 INFO @ Fri, 26 Jun 2020 07:54:33: 14000000 INFO @ Fri, 26 Jun 2020 07:54:36: 10000000 INFO @ Fri, 26 Jun 2020 07:54:37: 21000000 INFO @ Fri, 26 Jun 2020 07:54:40: 15000000 INFO @ Fri, 26 Jun 2020 07:54:43: 11000000 INFO @ Fri, 26 Jun 2020 07:54:44: 22000000 INFO @ Fri, 26 Jun 2020 07:54:48: 16000000 INFO @ Fri, 26 Jun 2020 07:54:50: 23000000 INFO @ Fri, 26 Jun 2020 07:54:50: 12000000 INFO @ Fri, 26 Jun 2020 07:54:55: 17000000 INFO @ Fri, 26 Jun 2020 07:54:57: 24000000 INFO @ Fri, 26 Jun 2020 07:54:57: 13000000 INFO @ Fri, 26 Jun 2020 07:55:01: 18000000 INFO @ Fri, 26 Jun 2020 07:55:03: 25000000 INFO @ Fri, 26 Jun 2020 07:55:04: 14000000 INFO @ Fri, 26 Jun 2020 07:55:07: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:55:07: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:55:07: #1 total tags in treatment: 25470512 INFO @ Fri, 26 Jun 2020 07:55:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:55:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:55:07: #1 tags after filtering in treatment: 25470512 INFO @ Fri, 26 Jun 2020 07:55:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:55:07: #1 finished! INFO @ Fri, 26 Jun 2020 07:55:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:55:08: 19000000 INFO @ Fri, 26 Jun 2020 07:55:09: #2 number of paired peaks: 150 WARNING @ Fri, 26 Jun 2020 07:55:09: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 26 Jun 2020 07:55:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:55:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:55:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:55:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:55:09: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:55:09: #2 alternative fragment length(s) may be 1,23,328,412,506,523,582,598 bps INFO @ Fri, 26 Jun 2020 07:55:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.05_model.r WARNING @ Fri, 26 Jun 2020 07:55:09: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:55:09: #2 You may need to consider one of the other alternative d(s): 1,23,328,412,506,523,582,598 WARNING @ Fri, 26 Jun 2020 07:55:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:55:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:55:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:55:11: 15000000 INFO @ Fri, 26 Jun 2020 07:55:15: 20000000 INFO @ Fri, 26 Jun 2020 07:55:17: 16000000 INFO @ Fri, 26 Jun 2020 07:55:21: 21000000 INFO @ Fri, 26 Jun 2020 07:55:24: 17000000 INFO @ Fri, 26 Jun 2020 07:55:28: 22000000 INFO @ Fri, 26 Jun 2020 07:55:30: 18000000 INFO @ Fri, 26 Jun 2020 07:55:34: 23000000 INFO @ Fri, 26 Jun 2020 07:55:37: 19000000 INFO @ Fri, 26 Jun 2020 07:55:41: 24000000 INFO @ Fri, 26 Jun 2020 07:55:43: 20000000 INFO @ Fri, 26 Jun 2020 07:55:47: 25000000 INFO @ Fri, 26 Jun 2020 07:55:50: 21000000 INFO @ Fri, 26 Jun 2020 07:55:51: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:55:51: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:55:51: #1 total tags in treatment: 25470512 INFO @ Fri, 26 Jun 2020 07:55:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:55:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:55:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:55:51: #1 tags after filtering in treatment: 25470512 INFO @ Fri, 26 Jun 2020 07:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:55:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:55:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:55:53: #2 number of paired peaks: 150 WARNING @ Fri, 26 Jun 2020 07:55:53: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 26 Jun 2020 07:55:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:55:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:55:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:55:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:55:53: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:55:53: #2 alternative fragment length(s) may be 1,23,328,412,506,523,582,598 bps INFO @ Fri, 26 Jun 2020 07:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.10_model.r WARNING @ Fri, 26 Jun 2020 07:55:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:55:53: #2 You may need to consider one of the other alternative d(s): 1,23,328,412,506,523,582,598 WARNING @ Fri, 26 Jun 2020 07:55:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:55:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:55:56: 22000000 INFO @ Fri, 26 Jun 2020 07:56:02: 23000000 INFO @ Fri, 26 Jun 2020 07:56:08: 24000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:56:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.05_summits.bed INFO @ Fri, 26 Jun 2020 07:56:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:56:14: 25000000 INFO @ Fri, 26 Jun 2020 07:56:17: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:56:17: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:56:17: #1 total tags in treatment: 25470512 INFO @ Fri, 26 Jun 2020 07:56:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:56:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:56:18: #1 tags after filtering in treatment: 25470512 INFO @ Fri, 26 Jun 2020 07:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:56:18: #1 finished! INFO @ Fri, 26 Jun 2020 07:56:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:56:20: #2 number of paired peaks: 150 WARNING @ Fri, 26 Jun 2020 07:56:20: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Fri, 26 Jun 2020 07:56:20: start model_add_line... INFO @ Fri, 26 Jun 2020 07:56:20: start X-correlation... INFO @ Fri, 26 Jun 2020 07:56:20: end of X-cor INFO @ Fri, 26 Jun 2020 07:56:20: #2 finished! INFO @ Fri, 26 Jun 2020 07:56:20: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:56:20: #2 alternative fragment length(s) may be 1,23,328,412,506,523,582,598 bps INFO @ Fri, 26 Jun 2020 07:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.20_model.r WARNING @ Fri, 26 Jun 2020 07:56:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:56:20: #2 You may need to consider one of the other alternative d(s): 1,23,328,412,506,523,582,598 WARNING @ Fri, 26 Jun 2020 07:56:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:56:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:56:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:56:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:56:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:56:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.10_summits.bed INFO @ Fri, 26 Jun 2020 07:56:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:57:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494975/SRX494975.20_summits.bed INFO @ Fri, 26 Jun 2020 07:57:21: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling