Job ID = 6626425 SRX = SRX7630546 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41859759 spots for SRR10964908/SRR10964908.sra Written 41859759 spots for SRR10964908/SRR10964908.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626606 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:10 41859759 reads; of these: 41859759 (100.00%) were unpaired; of these: 15980614 (38.18%) aligned 0 times 21433163 (51.20%) aligned exactly 1 time 4445982 (10.62%) aligned >1 times 61.82% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 8235641 / 25879145 = 0.3182 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, 14 Jul 2020 07:13:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.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, 14 Jul 2020 07:13:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:13:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:13:28: 1000000 INFO @ Tue, 14 Jul 2020 07:13:32: 2000000 INFO @ Tue, 14 Jul 2020 07:13:37: 3000000 INFO @ Tue, 14 Jul 2020 07:13:41: 4000000 INFO @ Tue, 14 Jul 2020 07:13:46: 5000000 INFO @ Tue, 14 Jul 2020 07:13:50: 6000000 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, 14 Jul 2020 07:13:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.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, 14 Jul 2020 07:13:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:13:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:13:55: 7000000 INFO @ Tue, 14 Jul 2020 07:13:58: 1000000 INFO @ Tue, 14 Jul 2020 07:14:00: 8000000 INFO @ Tue, 14 Jul 2020 07:14:03: 2000000 INFO @ Tue, 14 Jul 2020 07:14:04: 9000000 INFO @ Tue, 14 Jul 2020 07:14:07: 3000000 INFO @ Tue, 14 Jul 2020 07:14:09: 10000000 INFO @ Tue, 14 Jul 2020 07:14:12: 4000000 INFO @ Tue, 14 Jul 2020 07:14:14: 11000000 INFO @ Tue, 14 Jul 2020 07:14:17: 5000000 INFO @ Tue, 14 Jul 2020 07:14:18: 12000000 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, 14 Jul 2020 07:14:21: 6000000 INFO @ Tue, 14 Jul 2020 07:14:23: 13000000 INFO @ Tue, 14 Jul 2020 07:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.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, 14 Jul 2020 07:14:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:14:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:14:26: 7000000 INFO @ Tue, 14 Jul 2020 07:14:28: 14000000 INFO @ Tue, 14 Jul 2020 07:14:28: 1000000 INFO @ Tue, 14 Jul 2020 07:14:31: 8000000 INFO @ Tue, 14 Jul 2020 07:14:32: 15000000 INFO @ Tue, 14 Jul 2020 07:14:32: 2000000 INFO @ Tue, 14 Jul 2020 07:14:35: 9000000 INFO @ Tue, 14 Jul 2020 07:14:37: 16000000 INFO @ Tue, 14 Jul 2020 07:14:37: 3000000 INFO @ Tue, 14 Jul 2020 07:14:40: 10000000 INFO @ Tue, 14 Jul 2020 07:14:41: 17000000 INFO @ Tue, 14 Jul 2020 07:14:42: 4000000 INFO @ Tue, 14 Jul 2020 07:14:44: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:14:44: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:14:44: #1 total tags in treatment: 17643504 INFO @ Tue, 14 Jul 2020 07:14:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:14:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:14:45: #1 tags after filtering in treatment: 17643504 INFO @ Tue, 14 Jul 2020 07:14:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:14:45: #1 finished! INFO @ Tue, 14 Jul 2020 07:14:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:14:45: 11000000 INFO @ Tue, 14 Jul 2020 07:14:46: #2 number of paired peaks: 315 WARNING @ Tue, 14 Jul 2020 07:14:46: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 14 Jul 2020 07:14:46: start model_add_line... INFO @ Tue, 14 Jul 2020 07:14:46: start X-correlation... INFO @ Tue, 14 Jul 2020 07:14:46: end of X-cor INFO @ Tue, 14 Jul 2020 07:14:46: #2 finished! INFO @ Tue, 14 Jul 2020 07:14:46: #2 predicted fragment length is 42 bps INFO @ Tue, 14 Jul 2020 07:14:46: #2 alternative fragment length(s) may be 2,42,562,596 bps INFO @ Tue, 14 Jul 2020 07:14:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.05_model.r WARNING @ Tue, 14 Jul 2020 07:14:46: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:14:46: #2 You may need to consider one of the other alternative d(s): 2,42,562,596 WARNING @ Tue, 14 Jul 2020 07:14:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:14:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:14:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:14:46: 5000000 INFO @ Tue, 14 Jul 2020 07:14:49: 12000000 INFO @ Tue, 14 Jul 2020 07:14:51: 6000000 INFO @ Tue, 14 Jul 2020 07:14:54: 13000000 INFO @ Tue, 14 Jul 2020 07:14:56: 7000000 INFO @ Tue, 14 Jul 2020 07:14:58: 14000000 INFO @ Tue, 14 Jul 2020 07:15:00: 8000000 INFO @ Tue, 14 Jul 2020 07:15:03: 15000000 INFO @ Tue, 14 Jul 2020 07:15:05: 9000000 INFO @ Tue, 14 Jul 2020 07:15:08: 16000000 INFO @ Tue, 14 Jul 2020 07:15:09: 10000000 INFO @ Tue, 14 Jul 2020 07:15:12: 17000000 INFO @ Tue, 14 Jul 2020 07:15:14: 11000000 INFO @ Tue, 14 Jul 2020 07:15:15: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:15:15: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:15:15: #1 total tags in treatment: 17643504 INFO @ Tue, 14 Jul 2020 07:15:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:15:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:15:15: #1 tags after filtering in treatment: 17643504 INFO @ Tue, 14 Jul 2020 07:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:15:15: #1 finished! INFO @ Tue, 14 Jul 2020 07:15:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:15:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:15:17: #2 number of paired peaks: 315 WARNING @ Tue, 14 Jul 2020 07:15:17: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 14 Jul 2020 07:15:17: start model_add_line... INFO @ Tue, 14 Jul 2020 07:15:17: start X-correlation... INFO @ Tue, 14 Jul 2020 07:15:17: end of X-cor INFO @ Tue, 14 Jul 2020 07:15:17: #2 finished! INFO @ Tue, 14 Jul 2020 07:15:17: #2 predicted fragment length is 42 bps INFO @ Tue, 14 Jul 2020 07:15:17: #2 alternative fragment length(s) may be 2,42,562,596 bps INFO @ Tue, 14 Jul 2020 07:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.10_model.r WARNING @ Tue, 14 Jul 2020 07:15:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:15:17: #2 You may need to consider one of the other alternative d(s): 2,42,562,596 WARNING @ Tue, 14 Jul 2020 07:15:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:15:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:15:18: 12000000 INFO @ Tue, 14 Jul 2020 07:15:23: 13000000 INFO @ Tue, 14 Jul 2020 07:15:28: 14000000 INFO @ Tue, 14 Jul 2020 07:15:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.05_summits.bed INFO @ Tue, 14 Jul 2020 07:15:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (864 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:15:32: 15000000 INFO @ Tue, 14 Jul 2020 07:15:37: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:15:41: 17000000 INFO @ Tue, 14 Jul 2020 07:15:44: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:15:44: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:15:44: #1 total tags in treatment: 17643504 INFO @ Tue, 14 Jul 2020 07:15:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:15:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:15:44: #1 tags after filtering in treatment: 17643504 INFO @ Tue, 14 Jul 2020 07:15:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:15:44: #1 finished! INFO @ Tue, 14 Jul 2020 07:15:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:15:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:15:45: #2 number of paired peaks: 315 WARNING @ Tue, 14 Jul 2020 07:15:45: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 14 Jul 2020 07:15:45: start model_add_line... INFO @ Tue, 14 Jul 2020 07:15:45: start X-correlation... INFO @ Tue, 14 Jul 2020 07:15:45: end of X-cor INFO @ Tue, 14 Jul 2020 07:15:45: #2 finished! INFO @ Tue, 14 Jul 2020 07:15:45: #2 predicted fragment length is 42 bps INFO @ Tue, 14 Jul 2020 07:15:45: #2 alternative fragment length(s) may be 2,42,562,596 bps INFO @ Tue, 14 Jul 2020 07:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.20_model.r WARNING @ Tue, 14 Jul 2020 07:15:46: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:15:46: #2 You may need to consider one of the other alternative d(s): 2,42,562,596 WARNING @ Tue, 14 Jul 2020 07:15:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:15:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:15:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:15:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.10_summits.bed INFO @ Tue, 14 Jul 2020 07:16:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (520 records, 4 fields): 69 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:16:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:16:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:16:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:16:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7630546/SRX7630546.20_summits.bed INFO @ Tue, 14 Jul 2020 07:16:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 27 millis CompletedMACS2peakCalling