Job ID = 12265487 SRX = SRX7196648 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11296081 spots for SRR10507710/SRR10507710.sra Written 11296081 spots for SRR10507710/SRR10507710.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265619 ("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: 00:04:09 11296081 reads; of these: 11296081 (100.00%) were unpaired; of these: 1616345 (14.31%) aligned 0 times 5352410 (47.38%) aligned exactly 1 time 4327326 (38.31%) aligned >1 times 85.69% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 3137763 / 9679736 = 0.3242 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.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 @ Sat, 03 Apr 2021 07:23:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:23:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:23:39: 1000000 INFO @ Sat, 03 Apr 2021 07:23:44: 2000000 INFO @ Sat, 03 Apr 2021 07:23:49: 3000000 INFO @ Sat, 03 Apr 2021 07:23:54: 4000000 INFO @ Sat, 03 Apr 2021 07:23:59: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:24:03: 6000000 INFO @ Sat, 03 Apr 2021 07:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.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 @ Sat, 03 Apr 2021 07:24:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:24:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:24:06: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:24:06: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:24:06: #1 total tags in treatment: 6541973 INFO @ Sat, 03 Apr 2021 07:24:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:24:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:24:06: #1 tags after filtering in treatment: 6541973 INFO @ Sat, 03 Apr 2021 07:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:24:06: #1 finished! INFO @ Sat, 03 Apr 2021 07:24:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:24:07: #2 number of paired peaks: 381 WARNING @ Sat, 03 Apr 2021 07:24:07: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Sat, 03 Apr 2021 07:24:07: start model_add_line... INFO @ Sat, 03 Apr 2021 07:24:07: start X-correlation... INFO @ Sat, 03 Apr 2021 07:24:07: end of X-cor INFO @ Sat, 03 Apr 2021 07:24:07: #2 finished! INFO @ Sat, 03 Apr 2021 07:24:07: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Apr 2021 07:24:07: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Apr 2021 07:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.05_model.r WARNING @ Sat, 03 Apr 2021 07:24:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:24:07: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Apr 2021 07:24:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:24:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:24:10: 1000000 INFO @ Sat, 03 Apr 2021 07:24:15: 2000000 INFO @ Sat, 03 Apr 2021 07:24:20: 3000000 INFO @ Sat, 03 Apr 2021 07:24:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:24:25: 4000000 INFO @ Sat, 03 Apr 2021 07:24:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:24:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:24:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.05_summits.bed INFO @ Sat, 03 Apr 2021 07:24:29: Done! INFO @ Sat, 03 Apr 2021 07:24:30: 5000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1586 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:24:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.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 @ Sat, 03 Apr 2021 07:24:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:24:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:24:35: 6000000 INFO @ Sat, 03 Apr 2021 07:24:38: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:24:38: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:24:38: #1 total tags in treatment: 6541973 INFO @ Sat, 03 Apr 2021 07:24:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:24:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:24:38: #1 tags after filtering in treatment: 6541973 INFO @ Sat, 03 Apr 2021 07:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:24:38: #1 finished! INFO @ Sat, 03 Apr 2021 07:24:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:24:39: #2 number of paired peaks: 381 WARNING @ Sat, 03 Apr 2021 07:24:39: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Sat, 03 Apr 2021 07:24:39: start model_add_line... INFO @ Sat, 03 Apr 2021 07:24:39: start X-correlation... INFO @ Sat, 03 Apr 2021 07:24:39: end of X-cor INFO @ Sat, 03 Apr 2021 07:24:39: #2 finished! INFO @ Sat, 03 Apr 2021 07:24:39: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Apr 2021 07:24:39: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Apr 2021 07:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.10_model.r WARNING @ Sat, 03 Apr 2021 07:24:39: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:24:39: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Apr 2021 07:24:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:24:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:24:39: 1000000 INFO @ Sat, 03 Apr 2021 07:24:44: 2000000 INFO @ Sat, 03 Apr 2021 07:24:49: 3000000 INFO @ Sat, 03 Apr 2021 07:24:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:24:54: 4000000 INFO @ Sat, 03 Apr 2021 07:24:59: 5000000 INFO @ Sat, 03 Apr 2021 07:25:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:25:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:25:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.10_summits.bed INFO @ Sat, 03 Apr 2021 07:25:01: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1128 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:25:04: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:25:07: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:25:07: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:25:07: #1 total tags in treatment: 6541973 INFO @ Sat, 03 Apr 2021 07:25:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:25:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:25:07: #1 tags after filtering in treatment: 6541973 INFO @ Sat, 03 Apr 2021 07:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:25:07: #1 finished! INFO @ Sat, 03 Apr 2021 07:25:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:25:08: #2 number of paired peaks: 381 WARNING @ Sat, 03 Apr 2021 07:25:08: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Sat, 03 Apr 2021 07:25:08: start model_add_line... INFO @ Sat, 03 Apr 2021 07:25:08: start X-correlation... INFO @ Sat, 03 Apr 2021 07:25:08: end of X-cor INFO @ Sat, 03 Apr 2021 07:25:08: #2 finished! INFO @ Sat, 03 Apr 2021 07:25:08: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Apr 2021 07:25:08: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 03 Apr 2021 07:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.20_model.r WARNING @ Sat, 03 Apr 2021 07:25:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:25:08: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 03 Apr 2021 07:25:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:25:08: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:25:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:25:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:25:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:25:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:25:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7196648/SRX7196648.20_summits.bed INFO @ Sat, 03 Apr 2021 07:25:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling