Job ID = 14167989 SRX = SRX8688960 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5418436 spots for SRR12174362/SRR12174362.sra Written 5418436 spots for SRR12174362/SRR12174362.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168528 ("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: 00:01:54 5418436 reads; of these: 5418436 (100.00%) were unpaired; of these: 650450 (12.00%) aligned 0 times 3418623 (63.09%) aligned exactly 1 time 1349363 (24.90%) aligned >1 times 88.00% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 213270 / 4767986 = 0.0447 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 14:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.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 14:13:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:13:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:13:55: 1000000 INFO @ Fri, 10 Dec 2021 14:14:01: 2000000 INFO @ Fri, 10 Dec 2021 14:14:07: 3000000 INFO @ Fri, 10 Dec 2021 14:14:13: 4000000 INFO @ Fri, 10 Dec 2021 14:14:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:14:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:14:17: #1 total tags in treatment: 4554716 INFO @ Fri, 10 Dec 2021 14:14:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:14:17: #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 14:14:17: #1 tags after filtering in treatment: 4554716 INFO @ Fri, 10 Dec 2021 14:14:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:14:17: #1 finished! INFO @ Fri, 10 Dec 2021 14:14:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:14:17: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 14:14:17: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 14:14:17: start model_add_line... INFO @ Fri, 10 Dec 2021 14:14:17: start X-correlation... INFO @ Fri, 10 Dec 2021 14:14:17: end of X-cor INFO @ Fri, 10 Dec 2021 14:14:17: #2 finished! INFO @ Fri, 10 Dec 2021 14:14:17: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:14:17: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:14:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.05_model.r WARNING @ Fri, 10 Dec 2021 14:14:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:14:17: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:14:17: #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 14:14:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:14:17: #3 Pre-compute pvalue-qvalue table... 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 14:14:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.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 14:14:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:14:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:14:25: 1000000 INFO @ Fri, 10 Dec 2021 14:14:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:14:31: 2000000 INFO @ Fri, 10 Dec 2021 14:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.05_summits.bed INFO @ Fri, 10 Dec 2021 14:14:32: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1020 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:14:37: 3000000 INFO @ Fri, 10 Dec 2021 14:14:43: 4000000 INFO @ Fri, 10 Dec 2021 14:14:47: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:14:47: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:14:47: #1 total tags in treatment: 4554716 INFO @ Fri, 10 Dec 2021 14:14:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:14:47: #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 14:14:47: #1 tags after filtering in treatment: 4554716 INFO @ Fri, 10 Dec 2021 14:14:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:14:47: #1 finished! INFO @ Fri, 10 Dec 2021 14:14:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:14:47: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 14:14:47: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 14:14:47: start model_add_line... INFO @ Fri, 10 Dec 2021 14:14:47: start X-correlation... INFO @ Fri, 10 Dec 2021 14:14:47: end of X-cor INFO @ Fri, 10 Dec 2021 14:14:47: #2 finished! INFO @ Fri, 10 Dec 2021 14:14:47: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:14:47: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:14:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.10_model.r WARNING @ Fri, 10 Dec 2021 14:14:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:14:47: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:14:47: #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 14:14:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:14:47: #3 Pre-compute pvalue-qvalue table... 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 14:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.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 14:14:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:14:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:14:55: 1000000 INFO @ Fri, 10 Dec 2021 14:14:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:15:01: 2000000 INFO @ Fri, 10 Dec 2021 14:15:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:15:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:15:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.10_summits.bed INFO @ Fri, 10 Dec 2021 14:15:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (799 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:15:07: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:15:13: 4000000 INFO @ Fri, 10 Dec 2021 14:15:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:15:16: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:15:16: #1 total tags in treatment: 4554716 INFO @ Fri, 10 Dec 2021 14:15:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:15:16: #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 14:15:16: #1 tags after filtering in treatment: 4554716 INFO @ Fri, 10 Dec 2021 14:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:15:16: #1 finished! INFO @ Fri, 10 Dec 2021 14:15:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:15:17: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 14:15:17: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 14:15:17: start model_add_line... INFO @ Fri, 10 Dec 2021 14:15:17: start X-correlation... INFO @ Fri, 10 Dec 2021 14:15:17: end of X-cor INFO @ Fri, 10 Dec 2021 14:15:17: #2 finished! INFO @ Fri, 10 Dec 2021 14:15:17: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:15:17: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.20_model.r WARNING @ Fri, 10 Dec 2021 14:15:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:15:17: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:15:17: #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 14:15:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:15:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:15:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688960/SRX8688960.20_summits.bed INFO @ Fri, 10 Dec 2021 14:15:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (495 records, 4 fields): 1 millis CompletedMACS2peakCalling