Job ID = 6368240 SRX = SRX494923 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:05 prefetch.2.10.7: 1) Downloading 'SRR1198455'... 2020-06-16T00:14:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:41 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:41 prefetch.2.10.7: 1) 'SRR1198455' was downloaded successfully Read 21771760 spots for SRR1198455/SRR1198455.sra Written 21771760 spots for SRR1198455/SRR1198455.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: 00:04:51 21771760 reads; of these: 21771760 (100.00%) were unpaired; of these: 1354744 (6.22%) aligned 0 times 17026428 (78.20%) aligned exactly 1 time 3390588 (15.57%) aligned >1 times 93.78% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 5572851 / 20417016 = 0.2730 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 09:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.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 09:27:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:43: 1000000 INFO @ Tue, 16 Jun 2020 09:27:49: 2000000 INFO @ Tue, 16 Jun 2020 09:27:55: 3000000 INFO @ Tue, 16 Jun 2020 09:28:01: 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 09:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.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 09:28:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:07: 5000000 INFO @ Tue, 16 Jun 2020 09:28:12: 1000000 INFO @ Tue, 16 Jun 2020 09:28:14: 6000000 INFO @ Tue, 16 Jun 2020 09:28:19: 2000000 INFO @ Tue, 16 Jun 2020 09:28:20: 7000000 INFO @ Tue, 16 Jun 2020 09:28:25: 3000000 INFO @ Tue, 16 Jun 2020 09:28:27: 8000000 INFO @ Tue, 16 Jun 2020 09:28:32: 4000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 09:28:34: 9000000 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 09:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.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 09:28:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:39: 5000000 INFO @ Tue, 16 Jun 2020 09:28:41: 10000000 INFO @ Tue, 16 Jun 2020 09:28:44: 1000000 INFO @ Tue, 16 Jun 2020 09:28:46: 6000000 INFO @ Tue, 16 Jun 2020 09:28:48: 11000000 INFO @ Tue, 16 Jun 2020 09:28:52: 2000000 INFO @ Tue, 16 Jun 2020 09:28:54: 7000000 INFO @ Tue, 16 Jun 2020 09:28:55: 12000000 INFO @ Tue, 16 Jun 2020 09:29:00: 3000000 INFO @ Tue, 16 Jun 2020 09:29:01: 8000000 INFO @ Tue, 16 Jun 2020 09:29:02: 13000000 INFO @ Tue, 16 Jun 2020 09:29:08: 4000000 INFO @ Tue, 16 Jun 2020 09:29:08: 9000000 INFO @ Tue, 16 Jun 2020 09:29:10: 14000000 INFO @ Tue, 16 Jun 2020 09:29:15: 10000000 INFO @ Tue, 16 Jun 2020 09:29:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:16: #1 total tags in treatment: 14844165 INFO @ Tue, 16 Jun 2020 09:29:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:16: #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 09:29:16: 5000000 INFO @ Tue, 16 Jun 2020 09:29:16: #1 tags after filtering in treatment: 14844165 INFO @ Tue, 16 Jun 2020 09:29:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:17: #2 number of paired peaks: 308 WARNING @ Tue, 16 Jun 2020 09:29:17: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:17: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:29:17: #2 alternative fragment length(s) may be 1,44,563 bps INFO @ Tue, 16 Jun 2020 09:29:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.05_model.r WARNING @ Tue, 16 Jun 2020 09:29:17: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:17: #2 You may need to consider one of the other alternative d(s): 1,44,563 WARNING @ Tue, 16 Jun 2020 09:29:17: #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 09:29:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:22: 11000000 INFO @ Tue, 16 Jun 2020 09:29:24: 6000000 INFO @ Tue, 16 Jun 2020 09:29:30: 12000000 INFO @ Tue, 16 Jun 2020 09:29:32: 7000000 INFO @ Tue, 16 Jun 2020 09:29:37: 13000000 INFO @ Tue, 16 Jun 2020 09:29:40: 8000000 INFO @ Tue, 16 Jun 2020 09:29:44: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:48: 9000000 INFO @ Tue, 16 Jun 2020 09:29:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:50: #1 total tags in treatment: 14844165 INFO @ Tue, 16 Jun 2020 09:29:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:50: #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 09:29:50: #1 tags after filtering in treatment: 14844165 INFO @ Tue, 16 Jun 2020 09:29:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:51: #2 number of paired peaks: 308 WARNING @ Tue, 16 Jun 2020 09:29:51: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:51: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:29:51: #2 alternative fragment length(s) may be 1,44,563 bps INFO @ Tue, 16 Jun 2020 09:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.10_model.r WARNING @ Tue, 16 Jun 2020 09:29:51: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:51: #2 You may need to consider one of the other alternative d(s): 1,44,563 WARNING @ Tue, 16 Jun 2020 09:29:51: #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 09:29:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:56: 10000000 INFO @ Tue, 16 Jun 2020 09:30:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.05_summits.bed INFO @ Tue, 16 Jun 2020 09:30:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (794 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:03: 11000000 INFO @ Tue, 16 Jun 2020 09:30:10: 12000000 INFO @ Tue, 16 Jun 2020 09:30:18: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:25: 14000000 INFO @ Tue, 16 Jun 2020 09:30:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:31: #1 total tags in treatment: 14844165 INFO @ Tue, 16 Jun 2020 09:30:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:31: #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 09:30:32: #1 tags after filtering in treatment: 14844165 INFO @ Tue, 16 Jun 2020 09:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:33: #2 number of paired peaks: 308 WARNING @ Tue, 16 Jun 2020 09:30:33: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:33: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:30:33: #2 alternative fragment length(s) may be 1,44,563 bps INFO @ Tue, 16 Jun 2020 09:30:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.20_model.r WARNING @ Tue, 16 Jun 2020 09:30:33: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:33: #2 You may need to consider one of the other alternative d(s): 1,44,563 WARNING @ Tue, 16 Jun 2020 09:30:33: #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 09:30:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494923/SRX494923.20_summits.bed INFO @ Tue, 16 Jun 2020 09:31:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 1 millis CompletedMACS2peakCalling