Job ID = 6368362 SRX = SRX495042 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:20 prefetch.2.10.7: 1) Downloading 'SRR1198574'... 2020-06-16T00:13:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:05 prefetch.2.10.7: 1) 'SRR1198574' was downloaded successfully Read 24434363 spots for SRR1198574/SRR1198574.sra Written 24434363 spots for SRR1198574/SRR1198574.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: 00:04:59 24434363 reads; of these: 24434363 (100.00%) were unpaired; of these: 3204890 (13.12%) aligned 0 times 17393152 (71.18%) aligned exactly 1 time 3836321 (15.70%) aligned >1 times 86.88% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 2473216 / 21229473 = 0.1165 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 09:29:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.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 09:29:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:28: 1000000 INFO @ Tue, 16 Jun 2020 09:29:34: 2000000 INFO @ Tue, 16 Jun 2020 09:29:39: 3000000 INFO @ Tue, 16 Jun 2020 09:29:45: 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 @ Tue, 16 Jun 2020 09:29:50: 5000000 INFO @ Tue, 16 Jun 2020 09:29:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.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 09:29:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:56: 6000000 INFO @ Tue, 16 Jun 2020 09:29:57: 1000000 INFO @ Tue, 16 Jun 2020 09:30:02: 7000000 INFO @ Tue, 16 Jun 2020 09:30:03: 2000000 INFO @ Tue, 16 Jun 2020 09:30:07: 8000000 INFO @ Tue, 16 Jun 2020 09:30:09: 3000000 INFO @ Tue, 16 Jun 2020 09:30:13: 9000000 INFO @ Tue, 16 Jun 2020 09:30:15: 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 @ Tue, 16 Jun 2020 09:30:19: 10000000 INFO @ Tue, 16 Jun 2020 09:30:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.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 09:30:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:21: 5000000 INFO @ Tue, 16 Jun 2020 09:30:25: 11000000 INFO @ Tue, 16 Jun 2020 09:30:27: 6000000 INFO @ Tue, 16 Jun 2020 09:30:27: 1000000 INFO @ Tue, 16 Jun 2020 09:30:31: 12000000 INFO @ Tue, 16 Jun 2020 09:30:33: 7000000 INFO @ Tue, 16 Jun 2020 09:30:34: 2000000 INFO @ Tue, 16 Jun 2020 09:30:37: 13000000 INFO @ Tue, 16 Jun 2020 09:30:40: 8000000 INFO @ Tue, 16 Jun 2020 09:30:40: 3000000 INFO @ Tue, 16 Jun 2020 09:30:43: 14000000 INFO @ Tue, 16 Jun 2020 09:30:46: 9000000 INFO @ Tue, 16 Jun 2020 09:30:47: 4000000 INFO @ Tue, 16 Jun 2020 09:30:50: 15000000 INFO @ Tue, 16 Jun 2020 09:30:52: 10000000 INFO @ Tue, 16 Jun 2020 09:30:53: 5000000 INFO @ Tue, 16 Jun 2020 09:30:56: 16000000 INFO @ Tue, 16 Jun 2020 09:30:58: 11000000 INFO @ Tue, 16 Jun 2020 09:31:00: 6000000 INFO @ Tue, 16 Jun 2020 09:31:02: 17000000 INFO @ Tue, 16 Jun 2020 09:31:05: 12000000 INFO @ Tue, 16 Jun 2020 09:31:06: 7000000 INFO @ Tue, 16 Jun 2020 09:31:08: 18000000 INFO @ Tue, 16 Jun 2020 09:31:11: 13000000 INFO @ Tue, 16 Jun 2020 09:31:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:13: #1 total tags in treatment: 18756257 INFO @ Tue, 16 Jun 2020 09:31:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:13: #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 09:31:13: 8000000 INFO @ Tue, 16 Jun 2020 09:31:13: #1 tags after filtering in treatment: 18756257 INFO @ Tue, 16 Jun 2020 09:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:14: #2 number of paired peaks: 246 WARNING @ Tue, 16 Jun 2020 09:31:14: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:15: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:31:15: #2 alternative fragment length(s) may be 1,37,545,577 bps INFO @ Tue, 16 Jun 2020 09:31:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.05_model.r WARNING @ Tue, 16 Jun 2020 09:31:15: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:15: #2 You may need to consider one of the other alternative d(s): 1,37,545,577 WARNING @ Tue, 16 Jun 2020 09:31:15: #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 09:31:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:17: 14000000 INFO @ Tue, 16 Jun 2020 09:31:19: 9000000 INFO @ Tue, 16 Jun 2020 09:31:23: 15000000 INFO @ Tue, 16 Jun 2020 09:31:25: 10000000 INFO @ Tue, 16 Jun 2020 09:31:29: 16000000 INFO @ Tue, 16 Jun 2020 09:31:32: 11000000 INFO @ Tue, 16 Jun 2020 09:31:35: 17000000 INFO @ Tue, 16 Jun 2020 09:31:38: 12000000 INFO @ Tue, 16 Jun 2020 09:31:41: 18000000 INFO @ Tue, 16 Jun 2020 09:31:44: 13000000 INFO @ Tue, 16 Jun 2020 09:31:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:46: #1 total tags in treatment: 18756257 INFO @ Tue, 16 Jun 2020 09:31:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:46: #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 09:31:46: #1 tags after filtering in treatment: 18756257 INFO @ Tue, 16 Jun 2020 09:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:47: #2 number of paired peaks: 246 WARNING @ Tue, 16 Jun 2020 09:31:47: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:48: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:31:48: #2 alternative fragment length(s) may be 1,37,545,577 bps INFO @ Tue, 16 Jun 2020 09:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:48: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:48: #2 You may need to consider one of the other alternative d(s): 1,37,545,577 WARNING @ Tue, 16 Jun 2020 09:31:48: #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 09:31:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:50: 14000000 INFO @ Tue, 16 Jun 2020 09:31:56: 15000000 INFO @ Tue, 16 Jun 2020 09:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (798 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:01: 16000000 INFO @ Tue, 16 Jun 2020 09:32:07: 17000000 INFO @ Tue, 16 Jun 2020 09:32:13: 18000000 INFO @ Tue, 16 Jun 2020 09:32:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:32:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:32:17: #1 total tags in treatment: 18756257 INFO @ Tue, 16 Jun 2020 09:32:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:17: #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 09:32:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:18: #1 tags after filtering in treatment: 18756257 INFO @ Tue, 16 Jun 2020 09:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:19: #2 number of paired peaks: 246 WARNING @ Tue, 16 Jun 2020 09:32:19: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:19: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:32:19: #2 alternative fragment length(s) may be 1,37,545,577 bps INFO @ Tue, 16 Jun 2020 09:32:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.20_model.r WARNING @ Tue, 16 Jun 2020 09:32:19: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:19: #2 You may need to consider one of the other alternative d(s): 1,37,545,577 WARNING @ Tue, 16 Jun 2020 09:32:19: #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 09:32:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (412 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495042/SRX495042.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 1 millis CompletedMACS2peakCalling