Job ID = 12265713 SRX = SRX7281027 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21439159 spots for SRR10601375/SRR10601375.sra Written 21439159 spots for SRR10601375/SRR10601375.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265925 ("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: 00:08:14 21439159 reads; of these: 21439159 (100.00%) were unpaired; of these: 9749323 (45.47%) aligned 0 times 9780594 (45.62%) aligned exactly 1 time 1909242 (8.91%) aligned >1 times 54.53% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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] 5217366 / 11689836 = 0.4463 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 08:31:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.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 08:31:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:31:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:32:01: 1000000 INFO @ Sat, 03 Apr 2021 08:32:07: 2000000 INFO @ Sat, 03 Apr 2021 08:32:13: 3000000 INFO @ Sat, 03 Apr 2021 08:32:19: 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 08:32:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.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 08:32:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:32:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:32:26: 5000000 INFO @ Sat, 03 Apr 2021 08:32:31: 1000000 INFO @ Sat, 03 Apr 2021 08:32:32: 6000000 INFO @ Sat, 03 Apr 2021 08:32:36: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:32:36: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:32:36: #1 total tags in treatment: 6472470 INFO @ Sat, 03 Apr 2021 08:32:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:32:36: #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 08:32:36: #1 tags after filtering in treatment: 6472470 INFO @ Sat, 03 Apr 2021 08:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:32:36: #1 finished! INFO @ Sat, 03 Apr 2021 08:32:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:32:36: #2 number of paired peaks: 4637 INFO @ Sat, 03 Apr 2021 08:32:36: start model_add_line... INFO @ Sat, 03 Apr 2021 08:32:37: start X-correlation... INFO @ Sat, 03 Apr 2021 08:32:37: end of X-cor INFO @ Sat, 03 Apr 2021 08:32:37: #2 finished! INFO @ Sat, 03 Apr 2021 08:32:37: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 08:32:37: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Apr 2021 08:32:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.05_model.r WARNING @ Sat, 03 Apr 2021 08:32:37: #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 08:32:37: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Apr 2021 08:32:37: #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 08:32:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:32:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:32:37: 2000000 INFO @ Sat, 03 Apr 2021 08:32:43: 3000000 INFO @ Sat, 03 Apr 2021 08:32:49: 4000000 INFO @ Sat, 03 Apr 2021 08:32:50: #3 Call peaks for each chromosome... 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 08:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.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 08:32:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:32:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:32:56: 5000000 INFO @ Sat, 03 Apr 2021 08:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.05_summits.bed INFO @ Sat, 03 Apr 2021 08:32:59: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (18062 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:33:02: 1000000 INFO @ Sat, 03 Apr 2021 08:33:04: 6000000 INFO @ Sat, 03 Apr 2021 08:33:07: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:33:07: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:33:07: #1 total tags in treatment: 6472470 INFO @ Sat, 03 Apr 2021 08:33:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:33:07: #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 08:33:07: #1 tags after filtering in treatment: 6472470 INFO @ Sat, 03 Apr 2021 08:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:33:07: #1 finished! INFO @ Sat, 03 Apr 2021 08:33:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:33:08: #2 number of paired peaks: 4637 INFO @ Sat, 03 Apr 2021 08:33:08: start model_add_line... INFO @ Sat, 03 Apr 2021 08:33:08: start X-correlation... INFO @ Sat, 03 Apr 2021 08:33:08: end of X-cor INFO @ Sat, 03 Apr 2021 08:33:08: #2 finished! INFO @ Sat, 03 Apr 2021 08:33:08: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 08:33:08: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Apr 2021 08:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.10_model.r WARNING @ Sat, 03 Apr 2021 08:33:08: #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 08:33:08: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Apr 2021 08:33:08: #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 08:33:08: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:33:09: 2000000 INFO @ Sat, 03 Apr 2021 08:33:16: 3000000 INFO @ Sat, 03 Apr 2021 08:33:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:33:24: 4000000 INFO @ Sat, 03 Apr 2021 08:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.10_summits.bed INFO @ Sat, 03 Apr 2021 08:33:31: Done! INFO @ Sat, 03 Apr 2021 08:33:31: 5000000 pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11850 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:33:38: 6000000 INFO @ Sat, 03 Apr 2021 08:33:41: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:33:41: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:33:41: #1 total tags in treatment: 6472470 INFO @ Sat, 03 Apr 2021 08:33:41: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:33:41: #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 08:33:41: #1 tags after filtering in treatment: 6472470 INFO @ Sat, 03 Apr 2021 08:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:33:41: #1 finished! INFO @ Sat, 03 Apr 2021 08:33:41: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:33:42: #2 number of paired peaks: 4637 INFO @ Sat, 03 Apr 2021 08:33:42: start model_add_line... INFO @ Sat, 03 Apr 2021 08:33:42: start X-correlation... INFO @ Sat, 03 Apr 2021 08:33:42: end of X-cor INFO @ Sat, 03 Apr 2021 08:33:42: #2 finished! INFO @ Sat, 03 Apr 2021 08:33:42: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 08:33:42: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 03 Apr 2021 08:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.20_model.r WARNING @ Sat, 03 Apr 2021 08:33:42: #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 08:33:42: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 03 Apr 2021 08:33:42: #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 08:33:42: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:33:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:33:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281027/SRX7281027.20_summits.bed INFO @ Sat, 03 Apr 2021 08:34:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5546 records, 4 fields): 8 millis CompletedMACS2peakCalling