Job ID = 6626636 SRX = SRX7262571 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17228213 spots for SRR10582198/SRR10582198.sra Written 17228213 spots for SRR10582198/SRR10582198.sra Read 38054748 spots for SRR10582199/SRR10582199.sra Written 38054748 spots for SRR10582199/SRR10582199.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626803 ("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: 00:08:53 55282961 reads; of these: 55282961 (100.00%) were unpaired; of these: 49052561 (88.73%) aligned 0 times 4856531 (8.78%) aligned exactly 1 time 1373869 (2.49%) aligned >1 times 11.27% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 1395252 / 6230400 = 0.2239 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.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 @ Tue, 14 Jul 2020 08:19:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:19:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:19:39: 1000000 INFO @ Tue, 14 Jul 2020 08:19:45: 2000000 INFO @ Tue, 14 Jul 2020 08:19:52: 3000000 INFO @ Tue, 14 Jul 2020 08:19:58: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:20:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.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 @ Tue, 14 Jul 2020 08:20:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:20:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:20:04: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:20:04: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:20:04: #1 total tags in treatment: 4835148 INFO @ Tue, 14 Jul 2020 08:20:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:20:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:20:04: #1 tags after filtering in treatment: 4835148 INFO @ Tue, 14 Jul 2020 08:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:20:04: #1 finished! INFO @ Tue, 14 Jul 2020 08:20:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:20:05: #2 number of paired peaks: 7530 INFO @ Tue, 14 Jul 2020 08:20:05: start model_add_line... INFO @ Tue, 14 Jul 2020 08:20:05: start X-correlation... INFO @ Tue, 14 Jul 2020 08:20:05: end of X-cor INFO @ Tue, 14 Jul 2020 08:20:05: #2 finished! INFO @ Tue, 14 Jul 2020 08:20:05: #2 predicted fragment length is 136 bps INFO @ Tue, 14 Jul 2020 08:20:05: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 14 Jul 2020 08:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.05_model.r WARNING @ Tue, 14 Jul 2020 08:20:05: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:20:05: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 14 Jul 2020 08:20:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:20:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:20:10: 1000000 INFO @ Tue, 14 Jul 2020 08:20:17: 2000000 INFO @ Tue, 14 Jul 2020 08:20:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.05_summits.bed INFO @ Tue, 14 Jul 2020 08:20:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6363 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:20:24: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:20:31: 4000000 INFO @ Tue, 14 Jul 2020 08:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.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 @ Tue, 14 Jul 2020 08:20:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:20:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:20:38: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:20:38: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:20:38: #1 total tags in treatment: 4835148 INFO @ Tue, 14 Jul 2020 08:20:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:20:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:20:38: #1 tags after filtering in treatment: 4835148 INFO @ Tue, 14 Jul 2020 08:20:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:20:38: #1 finished! INFO @ Tue, 14 Jul 2020 08:20:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:20:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:20:38: #2 number of paired peaks: 7530 INFO @ Tue, 14 Jul 2020 08:20:38: start model_add_line... INFO @ Tue, 14 Jul 2020 08:20:39: start X-correlation... INFO @ Tue, 14 Jul 2020 08:20:39: end of X-cor INFO @ Tue, 14 Jul 2020 08:20:39: #2 finished! INFO @ Tue, 14 Jul 2020 08:20:39: #2 predicted fragment length is 136 bps INFO @ Tue, 14 Jul 2020 08:20:39: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 14 Jul 2020 08:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.10_model.r WARNING @ Tue, 14 Jul 2020 08:20:39: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:20:39: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 14 Jul 2020 08:20:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:20:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:20:40: 1000000 INFO @ Tue, 14 Jul 2020 08:20:48: 2000000 INFO @ Tue, 14 Jul 2020 08:20:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:20:55: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:20:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:20:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:20:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.10_summits.bed INFO @ Tue, 14 Jul 2020 08:20:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4212 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:21:01: 4000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:21:07: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:21:07: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:21:07: #1 total tags in treatment: 4835148 INFO @ Tue, 14 Jul 2020 08:21:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:21:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:21:07: #1 tags after filtering in treatment: 4835148 INFO @ Tue, 14 Jul 2020 08:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:21:07: #1 finished! INFO @ Tue, 14 Jul 2020 08:21:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:21:07: #2 number of paired peaks: 7530 INFO @ Tue, 14 Jul 2020 08:21:07: start model_add_line... INFO @ Tue, 14 Jul 2020 08:21:07: start X-correlation... INFO @ Tue, 14 Jul 2020 08:21:07: end of X-cor INFO @ Tue, 14 Jul 2020 08:21:07: #2 finished! INFO @ Tue, 14 Jul 2020 08:21:07: #2 predicted fragment length is 136 bps INFO @ Tue, 14 Jul 2020 08:21:07: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 14 Jul 2020 08:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.20_model.r WARNING @ Tue, 14 Jul 2020 08:21:07: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:21:07: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 14 Jul 2020 08:21:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:21:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:21:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:21:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:21:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:21:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262571/SRX7262571.20_summits.bed INFO @ Tue, 14 Jul 2020 08:21:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2372 records, 4 fields): 11 millis CompletedMACS2peakCalling