Job ID = 12264840 SRX = SRX2661682 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24528274 spots for SRR5366413/SRR5366413.sra Written 24528274 spots for SRR5366413/SRR5366413.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265101 ("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: 00:06:27 24528274 reads; of these: 24528274 (100.00%) were unpaired; of these: 1514986 (6.18%) aligned 0 times 18966867 (77.33%) aligned exactly 1 time 4046421 (16.50%) aligned >1 times 93.82% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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 12 files... [bam_rmdupse_core] 10266056 / 23013288 = 0.4461 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 06:07:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.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 06:07:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:15: 1000000 INFO @ Sat, 03 Apr 2021 06:07:23: 2000000 INFO @ Sat, 03 Apr 2021 06:07:30: 3000000 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 06:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.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 06:07:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:38: 4000000 INFO @ Sat, 03 Apr 2021 06:07:45: 1000000 INFO @ Sat, 03 Apr 2021 06:07:46: 5000000 INFO @ Sat, 03 Apr 2021 06:07:51: 2000000 INFO @ Sat, 03 Apr 2021 06:07:53: 6000000 INFO @ Sat, 03 Apr 2021 06:07:58: 3000000 INFO @ Sat, 03 Apr 2021 06:08:01: 7000000 BedGraph に変換中... INFO @ Sat, 03 Apr 2021 06:08:05: 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 06:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.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 06:08:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:08:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:08:08: 8000000 INFO @ Sat, 03 Apr 2021 06:08:12: 5000000 INFO @ Sat, 03 Apr 2021 06:08:15: 9000000 INFO @ Sat, 03 Apr 2021 06:08:16: 1000000 INFO @ Sat, 03 Apr 2021 06:08:19: 6000000 INFO @ Sat, 03 Apr 2021 06:08:23: 10000000 INFO @ Sat, 03 Apr 2021 06:08:23: 2000000 INFO @ Sat, 03 Apr 2021 06:08:26: 7000000 INFO @ Sat, 03 Apr 2021 06:08:30: 11000000 INFO @ Sat, 03 Apr 2021 06:08:31: 3000000 INFO @ Sat, 03 Apr 2021 06:08:33: 8000000 INFO @ Sat, 03 Apr 2021 06:08:37: 12000000 INFO @ Sat, 03 Apr 2021 06:08:39: 4000000 INFO @ Sat, 03 Apr 2021 06:08:39: 9000000 INFO @ Sat, 03 Apr 2021 06:08:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:08:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:08:43: #1 total tags in treatment: 12747232 INFO @ Sat, 03 Apr 2021 06:08:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:43: #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 06:08:43: #1 tags after filtering in treatment: 12747232 INFO @ Sat, 03 Apr 2021 06:08:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:08:43: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:44: #2 number of paired peaks: 1943 INFO @ Sat, 03 Apr 2021 06:08:44: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:44: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:44: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:44: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:44: #2 predicted fragment length is 72 bps INFO @ Sat, 03 Apr 2021 06:08:44: #2 alternative fragment length(s) may be 72 bps INFO @ Sat, 03 Apr 2021 06:08:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.05_model.r WARNING @ Sat, 03 Apr 2021 06:08:44: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:44: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sat, 03 Apr 2021 06:08:44: #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 06:08:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:46: 10000000 INFO @ Sat, 03 Apr 2021 06:08:47: 5000000 INFO @ Sat, 03 Apr 2021 06:08:53: 11000000 INFO @ Sat, 03 Apr 2021 06:08:54: 6000000 INFO @ Sat, 03 Apr 2021 06:08:59: 12000000 INFO @ Sat, 03 Apr 2021 06:09:01: 7000000 INFO @ Sat, 03 Apr 2021 06:09:04: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:09:04: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:09:04: #1 total tags in treatment: 12747232 INFO @ Sat, 03 Apr 2021 06:09:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:09:04: #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 06:09:05: #1 tags after filtering in treatment: 12747232 INFO @ Sat, 03 Apr 2021 06:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:09:05: #1 finished! INFO @ Sat, 03 Apr 2021 06:09:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:09:06: #2 number of paired peaks: 1943 INFO @ Sat, 03 Apr 2021 06:09:06: start model_add_line... INFO @ Sat, 03 Apr 2021 06:09:06: start X-correlation... INFO @ Sat, 03 Apr 2021 06:09:06: end of X-cor INFO @ Sat, 03 Apr 2021 06:09:06: #2 finished! INFO @ Sat, 03 Apr 2021 06:09:06: #2 predicted fragment length is 72 bps INFO @ Sat, 03 Apr 2021 06:09:06: #2 alternative fragment length(s) may be 72 bps INFO @ Sat, 03 Apr 2021 06:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.10_model.r WARNING @ Sat, 03 Apr 2021 06:09:06: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:09:06: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sat, 03 Apr 2021 06:09:06: #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 06:09:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:09:09: 8000000 INFO @ Sat, 03 Apr 2021 06:09:16: 9000000 INFO @ Sat, 03 Apr 2021 06:09:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:09:23: 10000000 INFO @ Sat, 03 Apr 2021 06:09:30: 11000000 INFO @ Sat, 03 Apr 2021 06:09:37: 12000000 INFO @ Sat, 03 Apr 2021 06:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.05_summits.bed INFO @ Sat, 03 Apr 2021 06:09:38: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (20091 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:09:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:09:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:09:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:09:43: #1 total tags in treatment: 12747232 INFO @ Sat, 03 Apr 2021 06:09:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:09:43: #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 06:09:43: #1 tags after filtering in treatment: 12747232 INFO @ Sat, 03 Apr 2021 06:09:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:09:43: #1 finished! INFO @ Sat, 03 Apr 2021 06:09:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:09:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:09:44: #2 number of paired peaks: 1943 INFO @ Sat, 03 Apr 2021 06:09:44: start model_add_line... INFO @ Sat, 03 Apr 2021 06:09:44: start X-correlation... INFO @ Sat, 03 Apr 2021 06:09:44: end of X-cor INFO @ Sat, 03 Apr 2021 06:09:44: #2 finished! INFO @ Sat, 03 Apr 2021 06:09:44: #2 predicted fragment length is 72 bps INFO @ Sat, 03 Apr 2021 06:09:44: #2 alternative fragment length(s) may be 72 bps INFO @ Sat, 03 Apr 2021 06:09:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.20_model.r WARNING @ Sat, 03 Apr 2021 06:09:44: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:09:44: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sat, 03 Apr 2021 06:09:44: #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 06:09:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:09:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.10_summits.bed INFO @ Sat, 03 Apr 2021 06:09:59: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12330 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:10:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2661682/SRX2661682.20_summits.bed INFO @ Sat, 03 Apr 2021 06:10:37: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4575 records, 4 fields): 12 millis CompletedMACS2peakCalling