Job ID = 12265696 SRX = SRX7281016 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22100297 spots for SRR10601364/SRR10601364.sra Written 22100297 spots for SRR10601364/SRR10601364.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265901 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:31 22100297 reads; of these: 22100297 (100.00%) were unpaired; of these: 11252922 (50.92%) aligned 0 times 7953827 (35.99%) aligned exactly 1 time 2893548 (13.09%) aligned >1 times 49.08% overall alignment rate Time searching: 00:11:32 Overall time: 00:11:32 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4727203 / 10847375 = 0.4358 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 08:29:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.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 08:29:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:29:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:29:22: 1000000 INFO @ Sat, 03 Apr 2021 08:29:29: 2000000 INFO @ Sat, 03 Apr 2021 08:29:35: 3000000 INFO @ Sat, 03 Apr 2021 08:29:42: 4000000 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 08:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.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 08:29:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:29:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:29:48: 5000000 INFO @ Sat, 03 Apr 2021 08:29:53: 1000000 INFO @ Sat, 03 Apr 2021 08:29:55: 6000000 INFO @ Sat, 03 Apr 2021 08:29:56: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:29:56: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:29:56: #1 total tags in treatment: 6120172 INFO @ Sat, 03 Apr 2021 08:29:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:29:56: #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 08:29:56: #1 tags after filtering in treatment: 6120172 INFO @ Sat, 03 Apr 2021 08:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:29:56: #1 finished! INFO @ Sat, 03 Apr 2021 08:29:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:29:56: #2 number of paired peaks: 762 WARNING @ Sat, 03 Apr 2021 08:29:56: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Sat, 03 Apr 2021 08:29:56: start model_add_line... INFO @ Sat, 03 Apr 2021 08:29:57: start X-correlation... INFO @ Sat, 03 Apr 2021 08:29:57: end of X-cor INFO @ Sat, 03 Apr 2021 08:29:57: #2 finished! INFO @ Sat, 03 Apr 2021 08:29:57: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 08:29:57: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Apr 2021 08:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.05_model.r WARNING @ Sat, 03 Apr 2021 08:29:57: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:29:57: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Apr 2021 08:29:57: #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 08:29:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:29:59: 2000000 INFO @ Sat, 03 Apr 2021 08:30:06: 3000000 INFO @ Sat, 03 Apr 2021 08:30:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:30:12: 4000000 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 08:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.05_summits.bed INFO @ Sat, 03 Apr 2021 08:30:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6862 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.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 08:30:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:30:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:30:19: 5000000 INFO @ Sat, 03 Apr 2021 08:30:22: 1000000 INFO @ Sat, 03 Apr 2021 08:30:26: 6000000 INFO @ Sat, 03 Apr 2021 08:30:26: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:30:26: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:30:26: #1 total tags in treatment: 6120172 INFO @ Sat, 03 Apr 2021 08:30:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:30:26: #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 08:30:26: #1 tags after filtering in treatment: 6120172 INFO @ Sat, 03 Apr 2021 08:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:30:26: #1 finished! INFO @ Sat, 03 Apr 2021 08:30:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:30:27: #2 number of paired peaks: 762 WARNING @ Sat, 03 Apr 2021 08:30:27: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Sat, 03 Apr 2021 08:30:27: start model_add_line... INFO @ Sat, 03 Apr 2021 08:30:27: start X-correlation... INFO @ Sat, 03 Apr 2021 08:30:27: end of X-cor INFO @ Sat, 03 Apr 2021 08:30:27: #2 finished! INFO @ Sat, 03 Apr 2021 08:30:27: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 08:30:27: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Apr 2021 08:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.10_model.r WARNING @ Sat, 03 Apr 2021 08:30:27: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:30:27: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Apr 2021 08:30:27: #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 08:30:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:30:29: 2000000 INFO @ Sat, 03 Apr 2021 08:30:35: 3000000 INFO @ Sat, 03 Apr 2021 08:30:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:30:42: 4000000 INFO @ Sat, 03 Apr 2021 08:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.10_summits.bed INFO @ Sat, 03 Apr 2021 08:30:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3234 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:30:48: 5000000 INFO @ Sat, 03 Apr 2021 08:30:54: 6000000 INFO @ Sat, 03 Apr 2021 08:30:55: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:30:55: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:30:55: #1 total tags in treatment: 6120172 INFO @ Sat, 03 Apr 2021 08:30:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:30:55: #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 08:30:55: #1 tags after filtering in treatment: 6120172 INFO @ Sat, 03 Apr 2021 08:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:30:55: #1 finished! INFO @ Sat, 03 Apr 2021 08:30:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:30:56: #2 number of paired peaks: 762 WARNING @ Sat, 03 Apr 2021 08:30:56: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Sat, 03 Apr 2021 08:30:56: start model_add_line... INFO @ Sat, 03 Apr 2021 08:30:56: start X-correlation... INFO @ Sat, 03 Apr 2021 08:30:56: end of X-cor INFO @ Sat, 03 Apr 2021 08:30:56: #2 finished! INFO @ Sat, 03 Apr 2021 08:30:56: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 08:30:56: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Apr 2021 08:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.20_model.r WARNING @ Sat, 03 Apr 2021 08:30:56: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:30:56: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Apr 2021 08:30:56: #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 08:30:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:30:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:31:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281016/SRX7281016.20_summits.bed INFO @ Sat, 03 Apr 2021 08:31:14: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (759 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。