Job ID = 16437421 SRX = SRX15046046 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 33792601 spots for SRR18970070/SRR18970070.sra Written 33792601 spots for SRR18970070/SRR18970070.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437463 ("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: 00:04:53 33792601 reads; of these: 33792601 (100.00%) were unpaired; of these: 25347731 (75.01%) aligned 0 times 6674588 (19.75%) aligned exactly 1 time 1770282 (5.24%) aligned >1 times 24.99% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 1635215 / 8444870 = 0.1936 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.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 @ Tue, 02 Aug 2022 12:34:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:34:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:34:31: 1000000 INFO @ Tue, 02 Aug 2022 12:34:37: 2000000 INFO @ Tue, 02 Aug 2022 12:34:42: 3000000 INFO @ Tue, 02 Aug 2022 12:34:47: 4000000 INFO @ Tue, 02 Aug 2022 12:34:52: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.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 @ Tue, 02 Aug 2022 12:34:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:34:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:34:57: 6000000 INFO @ Tue, 02 Aug 2022 12:35:01: 1000000 INFO @ Tue, 02 Aug 2022 12:35:02: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:35:02: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:35:02: #1 total tags in treatment: 6809655 INFO @ Tue, 02 Aug 2022 12:35:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:35:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:35:02: #1 tags after filtering in treatment: 6809655 INFO @ Tue, 02 Aug 2022 12:35:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:35:02: #1 finished! INFO @ Tue, 02 Aug 2022 12:35:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:35:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:35:02: #2 number of paired peaks: 375 WARNING @ Tue, 02 Aug 2022 12:35:02: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 02 Aug 2022 12:35:02: start model_add_line... INFO @ Tue, 02 Aug 2022 12:35:02: start X-correlation... INFO @ Tue, 02 Aug 2022 12:35:02: end of X-cor INFO @ Tue, 02 Aug 2022 12:35:02: #2 finished! INFO @ Tue, 02 Aug 2022 12:35:02: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 12:35:02: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 12:35:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.05_model.r WARNING @ Tue, 02 Aug 2022 12:35:02: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:35:02: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 12:35:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:35:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:35:07: 2000000 INFO @ Tue, 02 Aug 2022 12:35:13: 3000000 INFO @ Tue, 02 Aug 2022 12:35:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:35:19: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:35:24: 5000000 INFO @ Tue, 02 Aug 2022 12:35:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:35:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:35:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.05_summits.bed INFO @ Tue, 02 Aug 2022 12:35:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2126 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.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 @ Tue, 02 Aug 2022 12:35:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:35:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:35:29: 6000000 INFO @ Tue, 02 Aug 2022 12:35:31: 1000000 INFO @ Tue, 02 Aug 2022 12:35:34: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:35:34: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:35:34: #1 total tags in treatment: 6809655 INFO @ Tue, 02 Aug 2022 12:35:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:35:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:35:34: #1 tags after filtering in treatment: 6809655 INFO @ Tue, 02 Aug 2022 12:35:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:35:34: #1 finished! INFO @ Tue, 02 Aug 2022 12:35:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:35:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:35:34: #2 number of paired peaks: 375 WARNING @ Tue, 02 Aug 2022 12:35:34: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 02 Aug 2022 12:35:34: start model_add_line... INFO @ Tue, 02 Aug 2022 12:35:34: start X-correlation... INFO @ Tue, 02 Aug 2022 12:35:34: end of X-cor INFO @ Tue, 02 Aug 2022 12:35:34: #2 finished! INFO @ Tue, 02 Aug 2022 12:35:34: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 12:35:34: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 12:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.10_model.r WARNING @ Tue, 02 Aug 2022 12:35:34: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:35:34: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 12:35:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:35:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:35:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:35:36: 2000000 INFO @ Tue, 02 Aug 2022 12:35:42: 3000000 INFO @ Tue, 02 Aug 2022 12:35:47: 4000000 INFO @ Tue, 02 Aug 2022 12:35:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:35:52: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:35:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:35:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:35:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.10_summits.bed INFO @ Tue, 02 Aug 2022 12:35:56: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1339 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:35:58: 6000000 INFO @ Tue, 02 Aug 2022 12:36:02: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:36:02: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:36:02: #1 total tags in treatment: 6809655 INFO @ Tue, 02 Aug 2022 12:36:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:36:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:36:02: #1 tags after filtering in treatment: 6809655 INFO @ Tue, 02 Aug 2022 12:36:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:36:02: #1 finished! INFO @ Tue, 02 Aug 2022 12:36:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:36:03: #2 number of paired peaks: 375 WARNING @ Tue, 02 Aug 2022 12:36:03: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 02 Aug 2022 12:36:03: start model_add_line... INFO @ Tue, 02 Aug 2022 12:36:03: start X-correlation... INFO @ Tue, 02 Aug 2022 12:36:03: end of X-cor INFO @ Tue, 02 Aug 2022 12:36:03: #2 finished! INFO @ Tue, 02 Aug 2022 12:36:03: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 12:36:03: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 12:36:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.20_model.r WARNING @ Tue, 02 Aug 2022 12:36:03: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:36:03: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 12:36:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:36:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:36:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:36:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:36:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:36:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:36:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15046046/SRX15046046.20_summits.bed INFO @ Tue, 02 Aug 2022 12:36:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (711 records, 4 fields): 66 millis CompletedMACS2peakCalling