Job ID = 14168008 SRX = SRX8688968 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7490023 spots for SRR12174264/SRR12174264.sra Written 7490023 spots for SRR12174264/SRR12174264.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168645 ("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: 00:02:28 7490023 reads; of these: 7490023 (100.00%) were unpaired; of these: 258283 (3.45%) aligned 0 times 5243675 (70.01%) aligned exactly 1 time 1988065 (26.54%) aligned >1 times 96.55% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 327364 / 7231740 = 0.0453 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 14:22:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.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 14:22:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:22:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:22:42: 1000000 INFO @ Fri, 10 Dec 2021 14:22:47: 2000000 INFO @ Fri, 10 Dec 2021 14:22:53: 3000000 INFO @ Fri, 10 Dec 2021 14:22:58: 4000000 INFO @ Fri, 10 Dec 2021 14:23:03: 5000000 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 14:23:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.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 14:23:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:23:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:23:09: 6000000 INFO @ Fri, 10 Dec 2021 14:23:14: 1000000 INFO @ Fri, 10 Dec 2021 14:23:15: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:23:15: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:23:15: #1 total tags in treatment: 6904376 INFO @ Fri, 10 Dec 2021 14:23:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:23:15: #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 14:23:15: #1 tags after filtering in treatment: 6904376 INFO @ Fri, 10 Dec 2021 14:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:23:15: #1 finished! INFO @ Fri, 10 Dec 2021 14:23:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:23:15: #2 number of paired peaks: 339 WARNING @ Fri, 10 Dec 2021 14:23:15: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 10 Dec 2021 14:23:15: start model_add_line... INFO @ Fri, 10 Dec 2021 14:23:15: start X-correlation... INFO @ Fri, 10 Dec 2021 14:23:15: end of X-cor INFO @ Fri, 10 Dec 2021 14:23:15: #2 finished! INFO @ Fri, 10 Dec 2021 14:23:15: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 14:23:15: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 14:23:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.05_model.r WARNING @ Fri, 10 Dec 2021 14:23:15: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:23:15: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 14:23:15: #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 14:23:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:23:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:23:20: 2000000 INFO @ Fri, 10 Dec 2021 14:23:27: 3000000 INFO @ Fri, 10 Dec 2021 14:23:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:23:33: 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 14:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.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 14:23:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:23:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:23:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:23:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:23:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.05_summits.bed INFO @ Fri, 10 Dec 2021 14:23:37: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1303 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:23:40: 5000000 INFO @ Fri, 10 Dec 2021 14:23:43: 1000000 INFO @ Fri, 10 Dec 2021 14:23:47: 6000000 INFO @ Fri, 10 Dec 2021 14:23:49: 2000000 INFO @ Fri, 10 Dec 2021 14:23:53: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:23:53: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:23:53: #1 total tags in treatment: 6904376 INFO @ Fri, 10 Dec 2021 14:23:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:23:53: #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 14:23:53: #1 tags after filtering in treatment: 6904376 INFO @ Fri, 10 Dec 2021 14:23:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:23:53: #1 finished! INFO @ Fri, 10 Dec 2021 14:23:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:23:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:23:54: #2 number of paired peaks: 339 WARNING @ Fri, 10 Dec 2021 14:23:54: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 10 Dec 2021 14:23:54: start model_add_line... INFO @ Fri, 10 Dec 2021 14:23:54: start X-correlation... INFO @ Fri, 10 Dec 2021 14:23:54: end of X-cor INFO @ Fri, 10 Dec 2021 14:23:54: #2 finished! INFO @ Fri, 10 Dec 2021 14:23:54: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 14:23:54: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 14:23:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.10_model.r WARNING @ Fri, 10 Dec 2021 14:23:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:23:54: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 14:23:54: #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 14:23:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:23:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:23:55: 3000000 INFO @ Fri, 10 Dec 2021 14:24:01: 4000000 INFO @ Fri, 10 Dec 2021 14:24:06: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:24:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:24:12: 6000000 INFO @ Fri, 10 Dec 2021 14:24:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:24:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:24:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.10_summits.bed INFO @ Fri, 10 Dec 2021 14:24:15: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1024 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:24:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:24:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:24:17: #1 total tags in treatment: 6904376 INFO @ Fri, 10 Dec 2021 14:24:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:24:17: #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 14:24:17: #1 tags after filtering in treatment: 6904376 INFO @ Fri, 10 Dec 2021 14:24:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:24:17: #1 finished! INFO @ Fri, 10 Dec 2021 14:24:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:24:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:24:18: #2 number of paired peaks: 339 WARNING @ Fri, 10 Dec 2021 14:24:18: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 10 Dec 2021 14:24:18: start model_add_line... INFO @ Fri, 10 Dec 2021 14:24:18: start X-correlation... INFO @ Fri, 10 Dec 2021 14:24:18: end of X-cor INFO @ Fri, 10 Dec 2021 14:24:18: #2 finished! INFO @ Fri, 10 Dec 2021 14:24:18: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 14:24:18: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 14:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.20_model.r WARNING @ Fri, 10 Dec 2021 14:24:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:24:18: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 14:24:18: #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 14:24:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:24:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:24:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688968/SRX8688968.20_summits.bed INFO @ Fri, 10 Dec 2021 14:24:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (748 records, 4 fields): 2 millis CompletedMACS2peakCalling