Job ID = 12265680 SRX = SRX7281004 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22132727 spots for SRR10601379/SRR10601379.sra Written 22132727 spots for SRR10601379/SRR10601379.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265814 ("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: 00:06:09 22132727 reads; of these: 22132727 (100.00%) were unpaired; of these: 12008761 (54.26%) aligned 0 times 8785425 (39.69%) aligned exactly 1 time 1338541 (6.05%) aligned >1 times 45.74% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 4867874 / 10123966 = 0.4808 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 08:17:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.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 08:17:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:17:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:17:08: 1000000 INFO @ Sat, 03 Apr 2021 08:17:14: 2000000 INFO @ Sat, 03 Apr 2021 08:17:21: 3000000 INFO @ Sat, 03 Apr 2021 08:17:28: 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 08:17:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.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 08:17:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:17:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:17:34: 5000000 INFO @ Sat, 03 Apr 2021 08:17:36: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:17:36: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:17:36: #1 total tags in treatment: 5256092 INFO @ Sat, 03 Apr 2021 08:17:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:17:36: #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 08:17:36: #1 tags after filtering in treatment: 5256092 INFO @ Sat, 03 Apr 2021 08:17:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:17:36: #1 finished! INFO @ Sat, 03 Apr 2021 08:17:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:17:37: #2 number of paired peaks: 6121 INFO @ Sat, 03 Apr 2021 08:17:37: start model_add_line... INFO @ Sat, 03 Apr 2021 08:17:37: start X-correlation... INFO @ Sat, 03 Apr 2021 08:17:37: end of X-cor INFO @ Sat, 03 Apr 2021 08:17:37: #2 finished! INFO @ Sat, 03 Apr 2021 08:17:37: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:17:37: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Apr 2021 08:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.05_model.r WARNING @ Sat, 03 Apr 2021 08:17:37: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:17:37: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Apr 2021 08:17:37: #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 08:17:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:17:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:17:38: 1000000 INFO @ Sat, 03 Apr 2021 08:17:45: 2000000 INFO @ Sat, 03 Apr 2021 08:17:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:17:51: 3000000 INFO @ Sat, 03 Apr 2021 08:17:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:17:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:17:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.05_summits.bed INFO @ Sat, 03 Apr 2021 08:17:55: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (18700 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:17:58: 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 08:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.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 08:18:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:18:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:18:04: 5000000 INFO @ Sat, 03 Apr 2021 08:18:06: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:18:06: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:18:06: #1 total tags in treatment: 5256092 INFO @ Sat, 03 Apr 2021 08:18:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:18:06: #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 08:18:06: #1 tags after filtering in treatment: 5256092 INFO @ Sat, 03 Apr 2021 08:18:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:18:06: #1 finished! INFO @ Sat, 03 Apr 2021 08:18:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:18:07: #2 number of paired peaks: 6121 INFO @ Sat, 03 Apr 2021 08:18:07: start model_add_line... INFO @ Sat, 03 Apr 2021 08:18:07: start X-correlation... INFO @ Sat, 03 Apr 2021 08:18:07: end of X-cor INFO @ Sat, 03 Apr 2021 08:18:07: #2 finished! INFO @ Sat, 03 Apr 2021 08:18:07: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:18:07: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Apr 2021 08:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.10_model.r WARNING @ Sat, 03 Apr 2021 08:18:07: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:18:07: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Apr 2021 08:18:07: #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 08:18:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:18:08: 1000000 INFO @ Sat, 03 Apr 2021 08:18:15: 2000000 INFO @ Sat, 03 Apr 2021 08:18:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:18:22: 3000000 INFO @ Sat, 03 Apr 2021 08:18:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:18:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:18:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.10_summits.bed INFO @ Sat, 03 Apr 2021 08:18:24: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12469 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:18:29: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:18:36: 5000000 INFO @ Sat, 03 Apr 2021 08:18:38: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:18:38: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:18:38: #1 total tags in treatment: 5256092 INFO @ Sat, 03 Apr 2021 08:18:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:18:38: #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 08:18:38: #1 tags after filtering in treatment: 5256092 INFO @ Sat, 03 Apr 2021 08:18:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:18:38: #1 finished! INFO @ Sat, 03 Apr 2021 08:18:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:18:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:18:38: #2 number of paired peaks: 6121 INFO @ Sat, 03 Apr 2021 08:18:38: start model_add_line... INFO @ Sat, 03 Apr 2021 08:18:38: start X-correlation... INFO @ Sat, 03 Apr 2021 08:18:38: end of X-cor INFO @ Sat, 03 Apr 2021 08:18:38: #2 finished! INFO @ Sat, 03 Apr 2021 08:18:38: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:18:38: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 03 Apr 2021 08:18:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.20_model.r WARNING @ Sat, 03 Apr 2021 08:18:38: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:18:38: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 03 Apr 2021 08:18:38: #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 08:18:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:18:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:18:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:18:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:18:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:18:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281004/SRX7281004.20_summits.bed INFO @ Sat, 03 Apr 2021 08:18:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5869 records, 4 fields): 17 millis CompletedMACS2peakCalling