Job ID = 14170091 SRX = SRX5007622 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4363461 spots for SRR8187837/SRR8187837.sra Written 4363461 spots for SRR8187837/SRR8187837.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170662 ("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: 00:03:49 4363461 reads; of these: 4363461 (100.00%) were unpaired; of these: 505175 (11.58%) aligned 0 times 3196866 (73.26%) aligned exactly 1 time 661420 (15.16%) aligned >1 times 88.42% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 2381779 / 3858286 = 0.6173 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 @ Sat, 11 Dec 2021 05:15:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.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, 11 Dec 2021 05:15:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:15:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:15:13: 1000000 INFO @ Sat, 11 Dec 2021 05:15:19: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 05:15:19: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 05:15:19: #1 total tags in treatment: 1476507 INFO @ Sat, 11 Dec 2021 05:15:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:15:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 05:15:19: #1 tags after filtering in treatment: 1476507 INFO @ Sat, 11 Dec 2021 05:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 05:15:19: #1 finished! INFO @ Sat, 11 Dec 2021 05:15:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:15:20: #2 number of paired peaks: 965 WARNING @ Sat, 11 Dec 2021 05:15:20: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Sat, 11 Dec 2021 05:15:20: start model_add_line... INFO @ Sat, 11 Dec 2021 05:15:20: start X-correlation... INFO @ Sat, 11 Dec 2021 05:15:20: end of X-cor INFO @ Sat, 11 Dec 2021 05:15:20: #2 finished! INFO @ Sat, 11 Dec 2021 05:15:20: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 05:15:20: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Dec 2021 05:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.05_model.r WARNING @ Sat, 11 Dec 2021 05:15:20: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:15:20: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 11 Dec 2021 05:15:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 05:15:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:15:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.05_peaks.xls INFO @ Sat, 11 Dec 2021 05:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.05_summits.bed INFO @ Sat, 11 Dec 2021 05:15:25: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (625 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 05:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.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, 11 Dec 2021 05:15:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:15:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:15:42: 1000000 INFO @ Sat, 11 Dec 2021 05:15:47: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 05:15:47: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 05:15:47: #1 total tags in treatment: 1476507 INFO @ Sat, 11 Dec 2021 05:15:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:15:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 05:15:47: #1 tags after filtering in treatment: 1476507 INFO @ Sat, 11 Dec 2021 05:15:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 05:15:47: #1 finished! INFO @ Sat, 11 Dec 2021 05:15:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:15:47: #2 number of paired peaks: 965 WARNING @ Sat, 11 Dec 2021 05:15:47: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Sat, 11 Dec 2021 05:15:47: start model_add_line... INFO @ Sat, 11 Dec 2021 05:15:47: start X-correlation... INFO @ Sat, 11 Dec 2021 05:15:47: end of X-cor INFO @ Sat, 11 Dec 2021 05:15:47: #2 finished! INFO @ Sat, 11 Dec 2021 05:15:47: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 05:15:47: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Dec 2021 05:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.10_model.r WARNING @ Sat, 11 Dec 2021 05:15:48: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:15:48: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 11 Dec 2021 05:15:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 05:15:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:15:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:15:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:15:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.10_peaks.xls INFO @ Sat, 11 Dec 2021 05:15:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:15:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.10_summits.bed INFO @ Sat, 11 Dec 2021 05:15:53: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (321 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 05:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.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, 11 Dec 2021 05:16:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:16:00: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 05:16:13: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 05:16:19: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 05:16:19: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 05:16:19: #1 total tags in treatment: 1476507 INFO @ Sat, 11 Dec 2021 05:16:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:16:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 05:16:19: #1 tags after filtering in treatment: 1476507 INFO @ Sat, 11 Dec 2021 05:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 05:16:19: #1 finished! INFO @ Sat, 11 Dec 2021 05:16:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:16:20: #2 number of paired peaks: 965 WARNING @ Sat, 11 Dec 2021 05:16:20: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Sat, 11 Dec 2021 05:16:20: start model_add_line... INFO @ Sat, 11 Dec 2021 05:16:20: start X-correlation... INFO @ Sat, 11 Dec 2021 05:16:20: end of X-cor INFO @ Sat, 11 Dec 2021 05:16:20: #2 finished! INFO @ Sat, 11 Dec 2021 05:16:20: #2 predicted fragment length is 168 bps INFO @ Sat, 11 Dec 2021 05:16:20: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 11 Dec 2021 05:16:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.20_model.r WARNING @ Sat, 11 Dec 2021 05:16:20: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:16:20: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Sat, 11 Dec 2021 05:16:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 05:16:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:16:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:16:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:16:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.20_peaks.xls INFO @ Sat, 11 Dec 2021 05:16:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:16:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5007622/SRX5007622.20_summits.bed INFO @ Sat, 11 Dec 2021 05:16:25: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 2 millis CompletedMACS2peakCalling