Job ID = 14167237 SRX = SRX8688902 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8347060 spots for SRR12174254/SRR12174254.sra Written 8347060 spots for SRR12174254/SRR12174254.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167782 ("srTdm6") 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: 00:03:05 8347060 reads; of these: 8347060 (100.00%) were unpaired; of these: 487236 (5.84%) aligned 0 times 5525579 (66.20%) aligned exactly 1 time 2334245 (27.96%) aligned >1 times 94.16% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 409587 / 7859824 = 0.0521 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 11:16:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:16:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:16:24: 1000000 INFO @ Fri, 10 Dec 2021 11:16:30: 2000000 INFO @ Fri, 10 Dec 2021 11:16:37: 3000000 INFO @ Fri, 10 Dec 2021 11:16:44: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:16:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 11:16:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:16:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:16:50: 5000000 INFO @ Fri, 10 Dec 2021 11:16:55: 1000000 INFO @ Fri, 10 Dec 2021 11:16:57: 6000000 INFO @ Fri, 10 Dec 2021 11:17:02: 2000000 INFO @ Fri, 10 Dec 2021 11:17:04: 7000000 INFO @ Fri, 10 Dec 2021 11:17:07: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:17:07: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:17:07: #1 total tags in treatment: 7450237 INFO @ Fri, 10 Dec 2021 11:17:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:17:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:17:07: #1 tags after filtering in treatment: 7450237 INFO @ Fri, 10 Dec 2021 11:17:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:17:07: #1 finished! INFO @ Fri, 10 Dec 2021 11:17:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:17:07: #2 number of paired peaks: 167 WARNING @ Fri, 10 Dec 2021 11:17:07: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 10 Dec 2021 11:17:07: start model_add_line... INFO @ Fri, 10 Dec 2021 11:17:07: start X-correlation... INFO @ Fri, 10 Dec 2021 11:17:08: end of X-cor INFO @ Fri, 10 Dec 2021 11:17:08: #2 finished! INFO @ Fri, 10 Dec 2021 11:17:08: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 11:17:08: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Dec 2021 11:17:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.05_model.r WARNING @ Fri, 10 Dec 2021 11:17:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:17:08: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Dec 2021 11:17:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:17:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:17:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:17:09: 3000000 INFO @ Fri, 10 Dec 2021 11:17:15: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:17:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 11:17:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:17:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:17:22: 5000000 INFO @ Fri, 10 Dec 2021 11:17:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:17:24: 1000000 INFO @ Fri, 10 Dec 2021 11:17:28: 6000000 INFO @ Fri, 10 Dec 2021 11:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:17:31: 2000000 INFO @ Fri, 10 Dec 2021 11:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.05_summits.bed INFO @ Fri, 10 Dec 2021 11:17:31: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1257 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:17:35: 7000000 INFO @ Fri, 10 Dec 2021 11:17:38: 3000000 INFO @ Fri, 10 Dec 2021 11:17:38: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:17:38: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:17:38: #1 total tags in treatment: 7450237 INFO @ Fri, 10 Dec 2021 11:17:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:17:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:17:39: #1 tags after filtering in treatment: 7450237 INFO @ Fri, 10 Dec 2021 11:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:17:39: #1 finished! INFO @ Fri, 10 Dec 2021 11:17:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:17:39: #2 number of paired peaks: 167 WARNING @ Fri, 10 Dec 2021 11:17:39: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 10 Dec 2021 11:17:39: start model_add_line... INFO @ Fri, 10 Dec 2021 11:17:39: start X-correlation... INFO @ Fri, 10 Dec 2021 11:17:39: end of X-cor INFO @ Fri, 10 Dec 2021 11:17:39: #2 finished! INFO @ Fri, 10 Dec 2021 11:17:39: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 11:17:39: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Dec 2021 11:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.10_model.r WARNING @ Fri, 10 Dec 2021 11:17:39: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:17:39: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Dec 2021 11:17:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:17:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:17:45: 4000000 INFO @ Fri, 10 Dec 2021 11:17:51: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:17:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:17:57: 6000000 INFO @ Fri, 10 Dec 2021 11:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.10_summits.bed INFO @ Fri, 10 Dec 2021 11:18:03: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (959 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:18:04: 7000000 INFO @ Fri, 10 Dec 2021 11:18:07: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:18:07: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:18:07: #1 total tags in treatment: 7450237 INFO @ Fri, 10 Dec 2021 11:18:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:18:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:18:07: #1 tags after filtering in treatment: 7450237 INFO @ Fri, 10 Dec 2021 11:18:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:18:07: #1 finished! INFO @ Fri, 10 Dec 2021 11:18:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:18:07: #2 number of paired peaks: 167 WARNING @ Fri, 10 Dec 2021 11:18:07: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 10 Dec 2021 11:18:07: start model_add_line... INFO @ Fri, 10 Dec 2021 11:18:07: start X-correlation... INFO @ Fri, 10 Dec 2021 11:18:07: end of X-cor INFO @ Fri, 10 Dec 2021 11:18:07: #2 finished! INFO @ Fri, 10 Dec 2021 11:18:07: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 11:18:07: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Dec 2021 11:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.20_model.r WARNING @ Fri, 10 Dec 2021 11:18:07: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:18:07: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Dec 2021 11:18:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:18:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:18:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:18:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:18:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688902/SRX8688902.20_summits.bed INFO @ Fri, 10 Dec 2021 11:18:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (674 records, 4 fields): 2 millis CompletedMACS2peakCalling