Job ID = 6626377 SRX = SRX7262215 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9247400 spots for SRR10581838/SRR10581838.sra Written 9247400 spots for SRR10581838/SRR10581838.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626474 ("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: 00:02:11 9247400 reads; of these: 9247400 (100.00%) were unpaired; of these: 362288 (3.92%) aligned 0 times 7253084 (78.43%) aligned exactly 1 time 1632028 (17.65%) aligned >1 times 96.08% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 766497 / 8885112 = 0.0863 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 07:01:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.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 07:01:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:41: 1000000 INFO @ Tue, 14 Jul 2020 07:01:46: 2000000 INFO @ Tue, 14 Jul 2020 07:01:50: 3000000 INFO @ Tue, 14 Jul 2020 07:01:55: 4000000 INFO @ Tue, 14 Jul 2020 07:01:59: 5000000 INFO @ Tue, 14 Jul 2020 07:02:03: 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 07:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.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 07:02:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:02:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:02:08: 7000000 INFO @ Tue, 14 Jul 2020 07:02:11: 1000000 INFO @ Tue, 14 Jul 2020 07:02:12: 8000000 INFO @ Tue, 14 Jul 2020 07:02:13: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:02:13: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:02:13: #1 total tags in treatment: 8118615 INFO @ Tue, 14 Jul 2020 07:02:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:02:13: #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 07:02:13: #1 tags after filtering in treatment: 8118615 INFO @ Tue, 14 Jul 2020 07:02:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:02:13: #1 finished! INFO @ Tue, 14 Jul 2020 07:02:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:02:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:02:14: #2 number of paired peaks: 312 WARNING @ Tue, 14 Jul 2020 07:02:14: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Tue, 14 Jul 2020 07:02:14: start model_add_line... INFO @ Tue, 14 Jul 2020 07:02:14: start X-correlation... INFO @ Tue, 14 Jul 2020 07:02:14: end of X-cor INFO @ Tue, 14 Jul 2020 07:02:14: #2 finished! INFO @ Tue, 14 Jul 2020 07:02:14: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:02:14: #2 alternative fragment length(s) may be 4,46,522 bps INFO @ Tue, 14 Jul 2020 07:02:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.05_model.r WARNING @ Tue, 14 Jul 2020 07:02:14: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:02:14: #2 You may need to consider one of the other alternative d(s): 4,46,522 WARNING @ Tue, 14 Jul 2020 07:02:14: #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 07:02:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:02:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:02:16: 2000000 INFO @ Tue, 14 Jul 2020 07:02:21: 3000000 INFO @ Tue, 14 Jul 2020 07:02:26: 4000000 INFO @ Tue, 14 Jul 2020 07:02:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:02:31: 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, 14 Jul 2020 07:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.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 07:02:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:02:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:02:36: 6000000 INFO @ Tue, 14 Jul 2020 07:02:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.05_summits.bed INFO @ Tue, 14 Jul 2020 07:02:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (628 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:02:41: 1000000 INFO @ Tue, 14 Jul 2020 07:02:41: 7000000 INFO @ Tue, 14 Jul 2020 07:02:46: 2000000 INFO @ Tue, 14 Jul 2020 07:02:47: 8000000 INFO @ Tue, 14 Jul 2020 07:02:47: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:02:47: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:02:47: #1 total tags in treatment: 8118615 INFO @ Tue, 14 Jul 2020 07:02:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:02:47: #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 07:02:47: #1 tags after filtering in treatment: 8118615 INFO @ Tue, 14 Jul 2020 07:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:02:47: #1 finished! INFO @ Tue, 14 Jul 2020 07:02:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:02:48: #2 number of paired peaks: 312 WARNING @ Tue, 14 Jul 2020 07:02:48: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Tue, 14 Jul 2020 07:02:48: start model_add_line... INFO @ Tue, 14 Jul 2020 07:02:48: start X-correlation... INFO @ Tue, 14 Jul 2020 07:02:48: end of X-cor INFO @ Tue, 14 Jul 2020 07:02:48: #2 finished! INFO @ Tue, 14 Jul 2020 07:02:48: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:02:48: #2 alternative fragment length(s) may be 4,46,522 bps INFO @ Tue, 14 Jul 2020 07:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.10_model.r WARNING @ Tue, 14 Jul 2020 07:02:48: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:02:48: #2 You may need to consider one of the other alternative d(s): 4,46,522 WARNING @ Tue, 14 Jul 2020 07:02:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:02:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:02:51: 3000000 INFO @ Tue, 14 Jul 2020 07:02:56: 4000000 INFO @ Tue, 14 Jul 2020 07:03:01: 5000000 INFO @ Tue, 14 Jul 2020 07:03:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:03:06: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:03:11: 7000000 INFO @ Tue, 14 Jul 2020 07:03:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:03:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:03:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.10_summits.bed INFO @ Tue, 14 Jul 2020 07:03:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:03:16: 8000000 INFO @ Tue, 14 Jul 2020 07:03:17: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:03:17: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:03:17: #1 total tags in treatment: 8118615 INFO @ Tue, 14 Jul 2020 07:03:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:03:17: #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 07:03:17: #1 tags after filtering in treatment: 8118615 INFO @ Tue, 14 Jul 2020 07:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:03:17: #1 finished! INFO @ Tue, 14 Jul 2020 07:03:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:03:17: #2 number of paired peaks: 312 WARNING @ Tue, 14 Jul 2020 07:03:17: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Tue, 14 Jul 2020 07:03:17: start model_add_line... INFO @ Tue, 14 Jul 2020 07:03:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:03:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:03:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:03:18: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:03:18: #2 alternative fragment length(s) may be 4,46,522 bps INFO @ Tue, 14 Jul 2020 07:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.20_model.r WARNING @ Tue, 14 Jul 2020 07:03:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:03:18: #2 You may need to consider one of the other alternative d(s): 4,46,522 WARNING @ Tue, 14 Jul 2020 07:03:18: #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 07:03:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:03:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:03:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:03:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:03:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:03:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262215/SRX7262215.20_summits.bed INFO @ Tue, 14 Jul 2020 07:03:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 13 millis CompletedMACS2peakCalling