Job ID = 6366330 SRX = SRX113604 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:36:21 prefetch.2.10.7: 1) Downloading 'SRR393704'... 2020-06-15T22:36:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:37:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:37:18 prefetch.2.10.7: 'SRR393704' is valid 2020-06-15T22:37:18 prefetch.2.10.7: 1) 'SRR393704' was downloaded successfully Read 11039671 spots for SRR393704/SRR393704.sra Written 11039671 spots for SRR393704/SRR393704.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: 00:02:24 11039671 reads; of these: 11039671 (100.00%) were unpaired; of these: 566318 (5.13%) aligned 0 times 8160408 (73.92%) aligned exactly 1 time 2312945 (20.95%) aligned >1 times 94.87% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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_rmdupse_core] 2667994 / 10473353 = 0.2547 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 07:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.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 07:43:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:09: 1000000 INFO @ Tue, 16 Jun 2020 07:43:14: 2000000 INFO @ Tue, 16 Jun 2020 07:43:19: 3000000 INFO @ Tue, 16 Jun 2020 07:43:25: 4000000 INFO @ Tue, 16 Jun 2020 07:43:30: 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 07:43:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.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 07:43:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:35: 6000000 INFO @ Tue, 16 Jun 2020 07:43:39: 1000000 INFO @ Tue, 16 Jun 2020 07:43:40: 7000000 INFO @ Tue, 16 Jun 2020 07:43:44: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:43:44: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:43:44: #1 total tags in treatment: 7805359 INFO @ Tue, 16 Jun 2020 07:43:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:44: #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 07:43:44: #1 tags after filtering in treatment: 7805359 INFO @ Tue, 16 Jun 2020 07:43:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:44: 2000000 INFO @ Tue, 16 Jun 2020 07:43:45: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 07:43:45: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 07:43:45: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:45: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:45: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:45: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:45: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:43:45: #2 alternative fragment length(s) may be 0,39,96,118,133,173,200,269,355,499,534,549 bps INFO @ Tue, 16 Jun 2020 07:43:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.05_model.r WARNING @ Tue, 16 Jun 2020 07:43:45: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:43:45: #2 You may need to consider one of the other alternative d(s): 0,39,96,118,133,173,200,269,355,499,534,549 WARNING @ Tue, 16 Jun 2020 07:43:45: #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 07:43:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:49: 3000000 INFO @ Tue, 16 Jun 2020 07:43:55: 4000000 INFO @ Tue, 16 Jun 2020 07:44:00: 5000000 INFO @ Tue, 16 Jun 2020 07:44:00: #3 Call peaks for each chromosome... 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 07:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.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 07:44:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:05: 6000000 INFO @ Tue, 16 Jun 2020 07:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.05_summits.bed INFO @ Tue, 16 Jun 2020 07:44:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:09: 1000000 INFO @ Tue, 16 Jun 2020 07:44:10: 7000000 INFO @ Tue, 16 Jun 2020 07:44:14: 2000000 INFO @ Tue, 16 Jun 2020 07:44:14: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:44:14: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:44:14: #1 total tags in treatment: 7805359 INFO @ Tue, 16 Jun 2020 07:44:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:14: #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 07:44:14: #1 tags after filtering in treatment: 7805359 INFO @ Tue, 16 Jun 2020 07:44:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:15: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 07:44:15: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:15: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:15: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:15: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:15: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:15: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:44:15: #2 alternative fragment length(s) may be 0,39,96,118,133,173,200,269,355,499,534,549 bps INFO @ Tue, 16 Jun 2020 07:44:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.10_model.r WARNING @ Tue, 16 Jun 2020 07:44:15: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:44:15: #2 You may need to consider one of the other alternative d(s): 0,39,96,118,133,173,200,269,355,499,534,549 WARNING @ Tue, 16 Jun 2020 07:44:15: #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 07:44:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:19: 3000000 INFO @ Tue, 16 Jun 2020 07:44:24: 4000000 INFO @ Tue, 16 Jun 2020 07:44:29: 5000000 INFO @ Tue, 16 Jun 2020 07:44:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:34: 6000000 INFO @ Tue, 16 Jun 2020 07:44:39: 7000000 INFO @ Tue, 16 Jun 2020 07:44:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.10_summits.bed INFO @ Tue, 16 Jun 2020 07:44:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (76 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:43: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:44:43: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:44:43: #1 total tags in treatment: 7805359 INFO @ Tue, 16 Jun 2020 07:44:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:43: #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 07:44:43: #1 tags after filtering in treatment: 7805359 INFO @ Tue, 16 Jun 2020 07:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:44: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 07:44:44: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:44: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:44:44: #2 alternative fragment length(s) may be 0,39,96,118,133,173,200,269,355,499,534,549 bps INFO @ Tue, 16 Jun 2020 07:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.20_model.r WARNING @ Tue, 16 Jun 2020 07:44:44: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:44:44: #2 You may need to consider one of the other alternative d(s): 0,39,96,118,133,173,200,269,355,499,534,549 WARNING @ Tue, 16 Jun 2020 07:44:44: #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 07:44:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:45:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113604/SRX113604.20_summits.bed INFO @ Tue, 16 Jun 2020 07:45:09: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling