Job ID = 6366285 SRX = SRX1078710 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:39:51 prefetch.2.10.7: 1) Downloading 'SRR2084317'... 2020-06-15T22:39:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:43:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:43:22 prefetch.2.10.7: 1) 'SRR2084317' was downloaded successfully Read 30520033 spots for SRR2084317/SRR2084317.sra Written 30520033 spots for SRR2084317/SRR2084317.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: 00:06:53 30520033 reads; of these: 30520033 (100.00%) were unpaired; of these: 1807802 (5.92%) aligned 0 times 24180760 (79.23%) aligned exactly 1 time 4531471 (14.85%) aligned >1 times 94.08% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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] 4300119 / 28712231 = 0.1498 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 @ Tue, 16 Jun 2020 07:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.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 @ Tue, 16 Jun 2020 07:59:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:06: 1000000 INFO @ Tue, 16 Jun 2020 07:59:12: 2000000 INFO @ Tue, 16 Jun 2020 07:59:19: 3000000 INFO @ Tue, 16 Jun 2020 07:59:25: 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 @ Tue, 16 Jun 2020 07:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.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 @ Tue, 16 Jun 2020 07:59:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:59:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:59:31: 5000000 INFO @ Tue, 16 Jun 2020 07:59:36: 1000000 INFO @ Tue, 16 Jun 2020 07:59:37: 6000000 INFO @ Tue, 16 Jun 2020 07:59:42: 2000000 INFO @ Tue, 16 Jun 2020 07:59:44: 7000000 INFO @ Tue, 16 Jun 2020 07:59:49: 3000000 INFO @ Tue, 16 Jun 2020 07:59:50: 8000000 INFO @ Tue, 16 Jun 2020 07:59:55: 4000000 INFO @ Tue, 16 Jun 2020 07:59:56: 9000000 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 @ Tue, 16 Jun 2020 08:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.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 @ Tue, 16 Jun 2020 08:00:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:00:01: 5000000 INFO @ Tue, 16 Jun 2020 08:00:02: 10000000 INFO @ Tue, 16 Jun 2020 08:00:07: 1000000 INFO @ Tue, 16 Jun 2020 08:00:07: 6000000 INFO @ Tue, 16 Jun 2020 08:00:09: 11000000 INFO @ Tue, 16 Jun 2020 08:00:13: 2000000 INFO @ Tue, 16 Jun 2020 08:00:13: 7000000 INFO @ Tue, 16 Jun 2020 08:00:15: 12000000 INFO @ Tue, 16 Jun 2020 08:00:20: 8000000 INFO @ Tue, 16 Jun 2020 08:00:20: 3000000 INFO @ Tue, 16 Jun 2020 08:00:22: 13000000 INFO @ Tue, 16 Jun 2020 08:00:26: 9000000 INFO @ Tue, 16 Jun 2020 08:00:26: 4000000 INFO @ Tue, 16 Jun 2020 08:00:28: 14000000 INFO @ Tue, 16 Jun 2020 08:00:32: 10000000 INFO @ Tue, 16 Jun 2020 08:00:33: 5000000 INFO @ Tue, 16 Jun 2020 08:00:34: 15000000 INFO @ Tue, 16 Jun 2020 08:00:38: 11000000 INFO @ Tue, 16 Jun 2020 08:00:39: 6000000 INFO @ Tue, 16 Jun 2020 08:00:41: 16000000 INFO @ Tue, 16 Jun 2020 08:00:44: 12000000 INFO @ Tue, 16 Jun 2020 08:00:46: 7000000 INFO @ Tue, 16 Jun 2020 08:00:47: 17000000 INFO @ Tue, 16 Jun 2020 08:00:50: 13000000 INFO @ Tue, 16 Jun 2020 08:00:52: 8000000 INFO @ Tue, 16 Jun 2020 08:00:54: 18000000 INFO @ Tue, 16 Jun 2020 08:00:57: 14000000 INFO @ Tue, 16 Jun 2020 08:00:59: 9000000 INFO @ Tue, 16 Jun 2020 08:01:00: 19000000 INFO @ Tue, 16 Jun 2020 08:01:03: 15000000 INFO @ Tue, 16 Jun 2020 08:01:05: 10000000 INFO @ Tue, 16 Jun 2020 08:01:07: 20000000 INFO @ Tue, 16 Jun 2020 08:01:09: 16000000 INFO @ Tue, 16 Jun 2020 08:01:12: 11000000 INFO @ Tue, 16 Jun 2020 08:01:13: 21000000 INFO @ Tue, 16 Jun 2020 08:01:15: 17000000 INFO @ Tue, 16 Jun 2020 08:01:18: 12000000 INFO @ Tue, 16 Jun 2020 08:01:19: 22000000 INFO @ Tue, 16 Jun 2020 08:01:21: 18000000 INFO @ Tue, 16 Jun 2020 08:01:25: 13000000 INFO @ Tue, 16 Jun 2020 08:01:26: 23000000 INFO @ Tue, 16 Jun 2020 08:01:28: 19000000 INFO @ Tue, 16 Jun 2020 08:01:31: 14000000 INFO @ Tue, 16 Jun 2020 08:01:32: 24000000 INFO @ Tue, 16 Jun 2020 08:01:34: 20000000 INFO @ Tue, 16 Jun 2020 08:01:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:01:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:01:35: #1 total tags in treatment: 24412112 INFO @ Tue, 16 Jun 2020 08:01:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:01:35: #1 tags after filtering in treatment: 24412112 INFO @ Tue, 16 Jun 2020 08:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:37: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:01:37: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:37: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:01:37: #2 alternative fragment length(s) may be 1,47,397,477,515,553 bps INFO @ Tue, 16 Jun 2020 08:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.05_model.r WARNING @ Tue, 16 Jun 2020 08:01:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:01:37: #2 You may need to consider one of the other alternative d(s): 1,47,397,477,515,553 WARNING @ Tue, 16 Jun 2020 08:01:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:01:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:01:38: 15000000 INFO @ Tue, 16 Jun 2020 08:01:40: 21000000 INFO @ Tue, 16 Jun 2020 08:01:44: 16000000 INFO @ Tue, 16 Jun 2020 08:01:46: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:01:51: 17000000 INFO @ Tue, 16 Jun 2020 08:01:53: 23000000 INFO @ Tue, 16 Jun 2020 08:01:57: 18000000 INFO @ Tue, 16 Jun 2020 08:01:59: 24000000 INFO @ Tue, 16 Jun 2020 08:02:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:02: #1 total tags in treatment: 24412112 INFO @ Tue, 16 Jun 2020 08:02:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:02:02: #1 tags after filtering in treatment: 24412112 INFO @ Tue, 16 Jun 2020 08:02:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:03: 19000000 INFO @ Tue, 16 Jun 2020 08:02:04: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:02:04: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:04: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:02:04: #2 alternative fragment length(s) may be 1,47,397,477,515,553 bps INFO @ Tue, 16 Jun 2020 08:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.10_model.r WARNING @ Tue, 16 Jun 2020 08:02:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:04: #2 You may need to consider one of the other alternative d(s): 1,47,397,477,515,553 WARNING @ Tue, 16 Jun 2020 08:02:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:02:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:10: 20000000 INFO @ Tue, 16 Jun 2020 08:02:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:16: 21000000 INFO @ Tue, 16 Jun 2020 08:02:22: 22000000 INFO @ Tue, 16 Jun 2020 08:02:28: 23000000 INFO @ Tue, 16 Jun 2020 08:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:35: 24000000 INFO @ Tue, 16 Jun 2020 08:02:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:37: #1 total tags in treatment: 24412112 INFO @ Tue, 16 Jun 2020 08:02:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:02:38: #1 tags after filtering in treatment: 24412112 INFO @ Tue, 16 Jun 2020 08:02:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:39: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:02:39: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:39: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:02:39: #2 alternative fragment length(s) may be 1,47,397,477,515,553 bps INFO @ Tue, 16 Jun 2020 08:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.20_model.r WARNING @ Tue, 16 Jun 2020 08:02:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:39: #2 You may need to consider one of the other alternative d(s): 1,47,397,477,515,553 WARNING @ Tue, 16 Jun 2020 08:02:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:02:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:02:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.10_summits.bed INFO @ Tue, 16 Jun 2020 08:02:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078710/SRX1078710.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling