Job ID = 6366300 SRX = SRX1078724 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:39:21 prefetch.2.10.7: 1) Downloading 'SRR2084331'... 2020-06-15T22:39:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:42:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:42:11 prefetch.2.10.7: 1) 'SRR2084331' was downloaded successfully Read 27013036 spots for SRR2084331/SRR2084331.sra Written 27013036 spots for SRR2084331/SRR2084331.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: 00:06:18 27013036 reads; of these: 27013036 (100.00%) were unpaired; of these: 284013 (1.05%) aligned 0 times 22372470 (82.82%) aligned exactly 1 time 4356553 (16.13%) aligned >1 times 98.95% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 7399084 / 26729023 = 0.2768 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 07:56:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.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 07:56:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:11: 1000000 INFO @ Tue, 16 Jun 2020 07:56:16: 2000000 INFO @ Tue, 16 Jun 2020 07:56:21: 3000000 INFO @ Tue, 16 Jun 2020 07:56:26: 4000000 INFO @ Tue, 16 Jun 2020 07:56:31: 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 @ Tue, 16 Jun 2020 07:56:36: 6000000 INFO @ Tue, 16 Jun 2020 07:56:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.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 07:56:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:41: 7000000 INFO @ Tue, 16 Jun 2020 07:56:41: 1000000 INFO @ Tue, 16 Jun 2020 07:56:46: 8000000 INFO @ Tue, 16 Jun 2020 07:56:46: 2000000 INFO @ Tue, 16 Jun 2020 07:56:51: 9000000 INFO @ Tue, 16 Jun 2020 07:56:52: 3000000 INFO @ Tue, 16 Jun 2020 07:56:56: 10000000 INFO @ Tue, 16 Jun 2020 07:56:57: 4000000 INFO @ Tue, 16 Jun 2020 07:57:01: 11000000 INFO @ Tue, 16 Jun 2020 07:57:02: 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 @ Tue, 16 Jun 2020 07:57:06: 12000000 INFO @ Tue, 16 Jun 2020 07:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.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 07:57:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:07: 6000000 INFO @ Tue, 16 Jun 2020 07:57:11: 13000000 INFO @ Tue, 16 Jun 2020 07:57:12: 1000000 INFO @ Tue, 16 Jun 2020 07:57:12: 7000000 INFO @ Tue, 16 Jun 2020 07:57:16: 14000000 INFO @ Tue, 16 Jun 2020 07:57:17: 8000000 INFO @ Tue, 16 Jun 2020 07:57:17: 2000000 INFO @ Tue, 16 Jun 2020 07:57:21: 15000000 INFO @ Tue, 16 Jun 2020 07:57:22: 9000000 INFO @ Tue, 16 Jun 2020 07:57:22: 3000000 INFO @ Tue, 16 Jun 2020 07:57:26: 16000000 INFO @ Tue, 16 Jun 2020 07:57:27: 10000000 INFO @ Tue, 16 Jun 2020 07:57:27: 4000000 INFO @ Tue, 16 Jun 2020 07:57:31: 17000000 INFO @ Tue, 16 Jun 2020 07:57:32: 11000000 INFO @ Tue, 16 Jun 2020 07:57:32: 5000000 INFO @ Tue, 16 Jun 2020 07:57:36: 18000000 INFO @ Tue, 16 Jun 2020 07:57:37: 12000000 INFO @ Tue, 16 Jun 2020 07:57:38: 6000000 INFO @ Tue, 16 Jun 2020 07:57:41: 19000000 INFO @ Tue, 16 Jun 2020 07:57:42: 13000000 INFO @ Tue, 16 Jun 2020 07:57:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:57:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:57:43: #1 total tags in treatment: 19329939 INFO @ Tue, 16 Jun 2020 07:57:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:43: #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 07:57:43: 7000000 INFO @ Tue, 16 Jun 2020 07:57:43: #1 tags after filtering in treatment: 19329939 INFO @ Tue, 16 Jun 2020 07:57:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:44: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 07:57:44: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 07:57:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:45: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:45: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:45: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:45: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:57:45: #2 alternative fragment length(s) may be 1,42,570,573,597 bps INFO @ Tue, 16 Jun 2020 07:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.05_model.r WARNING @ Tue, 16 Jun 2020 07:57:45: #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 07:57:45: #2 You may need to consider one of the other alternative d(s): 1,42,570,573,597 WARNING @ Tue, 16 Jun 2020 07:57:45: #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 07:57:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:57:47: 14000000 INFO @ Tue, 16 Jun 2020 07:57:48: 8000000 INFO @ Tue, 16 Jun 2020 07:57:52: 15000000 INFO @ Tue, 16 Jun 2020 07:57:53: 9000000 INFO @ Tue, 16 Jun 2020 07:57:57: 16000000 INFO @ Tue, 16 Jun 2020 07:57:58: 10000000 INFO @ Tue, 16 Jun 2020 07:58:03: 17000000 INFO @ Tue, 16 Jun 2020 07:58:03: 11000000 INFO @ Tue, 16 Jun 2020 07:58:07: 18000000 INFO @ Tue, 16 Jun 2020 07:58:09: 12000000 INFO @ Tue, 16 Jun 2020 07:58:12: 19000000 INFO @ Tue, 16 Jun 2020 07:58:14: 13000000 INFO @ Tue, 16 Jun 2020 07:58:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:58:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:58:14: #1 total tags in treatment: 19329939 INFO @ Tue, 16 Jun 2020 07:58:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:14: #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 07:58:15: #1 tags after filtering in treatment: 19329939 INFO @ Tue, 16 Jun 2020 07:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:15: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:58:16: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 07:58:16: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 07:58:16: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:16: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:16: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:16: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:16: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:58:16: #2 alternative fragment length(s) may be 1,42,570,573,597 bps INFO @ Tue, 16 Jun 2020 07:58:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.10_model.r WARNING @ Tue, 16 Jun 2020 07:58:16: #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 07:58:16: #2 You may need to consider one of the other alternative d(s): 1,42,570,573,597 WARNING @ Tue, 16 Jun 2020 07:58:16: #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 07:58:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:58:19: 14000000 INFO @ Tue, 16 Jun 2020 07:58:24: 15000000 INFO @ Tue, 16 Jun 2020 07:58:29: 16000000 INFO @ Tue, 16 Jun 2020 07:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.05_summits.bed INFO @ Tue, 16 Jun 2020 07:58:30: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:58:34: 17000000 INFO @ Tue, 16 Jun 2020 07:58:39: 18000000 INFO @ Tue, 16 Jun 2020 07:58:44: 19000000 INFO @ Tue, 16 Jun 2020 07:58:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:58:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:58:45: #1 total tags in treatment: 19329939 INFO @ Tue, 16 Jun 2020 07:58:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:45: #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 07:58:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:58:46: #1 tags after filtering in treatment: 19329939 INFO @ Tue, 16 Jun 2020 07:58:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:46: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:47: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 07:58:47: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 07:58:47: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:47: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:47: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:47: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:47: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:58:47: #2 alternative fragment length(s) may be 1,42,570,573,597 bps INFO @ Tue, 16 Jun 2020 07:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.20_model.r WARNING @ Tue, 16 Jun 2020 07:58:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:58:47: #2 You may need to consider one of the other alternative d(s): 1,42,570,573,597 WARNING @ Tue, 16 Jun 2020 07:58:47: #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 07:58:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.10_summits.bed INFO @ Tue, 16 Jun 2020 07:59:00: 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。 INFO @ Tue, 16 Jun 2020 07:59:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078724/SRX1078724.20_summits.bed INFO @ Tue, 16 Jun 2020 07:59:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling