Job ID = 6458916 SRX = SRX5775921 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:49:07 prefetch.2.10.7: 1) Downloading 'SRR8997124'... 2020-06-21T12:49:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:22 prefetch.2.10.7: 1) 'SRR8997124' was downloaded successfully Read 22776004 spots for SRR8997124/SRR8997124.sra Written 22776004 spots for SRR8997124/SRR8997124.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:08 22776004 reads; of these: 22776004 (100.00%) were unpaired; of these: 9982226 (43.83%) aligned 0 times 9206886 (40.42%) aligned exactly 1 time 3586892 (15.75%) aligned >1 times 56.17% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 8787165 / 12793778 = 0.6868 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 @ Sun, 21 Jun 2020 22:03:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.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 @ Sun, 21 Jun 2020 22:03:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:46: 1000000 INFO @ Sun, 21 Jun 2020 22:03:52: 2000000 INFO @ Sun, 21 Jun 2020 22:03:59: 3000000 INFO @ Sun, 21 Jun 2020 22:04:06: 4000000 INFO @ Sun, 21 Jun 2020 22:04:06: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:04:06: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:04:06: #1 total tags in treatment: 4006613 INFO @ Sun, 21 Jun 2020 22:04:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:04:06: #1 tags after filtering in treatment: 4006603 INFO @ Sun, 21 Jun 2020 22:04:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:06: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:07: #2 number of paired peaks: 1680 INFO @ Sun, 21 Jun 2020 22:04:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:07: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 22:04:07: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 22:04:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:07: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:07: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 22:04:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:04:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:07: #3 Pre-compute pvalue-qvalue table... 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 @ Sun, 21 Jun 2020 22:04:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.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 @ Sun, 21 Jun 2020 22:04:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:16: 1000000 INFO @ Sun, 21 Jun 2020 22:04:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.05_summits.bed INFO @ Sun, 21 Jun 2020 22:04:20: Done! pass1 - making usageList (740 chroms): 1 millis pass2 - checking and writing primary data (2317 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:23: 2000000 INFO @ Sun, 21 Jun 2020 22:04:29: 3000000 INFO @ Sun, 21 Jun 2020 22:04:36: 4000000 INFO @ Sun, 21 Jun 2020 22:04:36: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:04:36: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:04:36: #1 total tags in treatment: 4006613 INFO @ Sun, 21 Jun 2020 22:04:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:04:36: #1 tags after filtering in treatment: 4006603 INFO @ Sun, 21 Jun 2020 22:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:36: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:37: #2 number of paired peaks: 1680 INFO @ Sun, 21 Jun 2020 22:04:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:37: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 22:04:37: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 22:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.10_model.r WARNING @ Sun, 21 Jun 2020 22:04:37: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:37: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 22:04:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:04:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:37: #3 Pre-compute pvalue-qvalue table... 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 @ Sun, 21 Jun 2020 22:04:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.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 @ Sun, 21 Jun 2020 22:04:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:46: 1000000 INFO @ Sun, 21 Jun 2020 22:04:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.10_summits.bed INFO @ Sun, 21 Jun 2020 22:04:51: Done! pass1 - making usageList (589 chroms): 1 millis pass2 - checking and writing primary data (1631 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:52: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:04:59: 3000000 INFO @ Sun, 21 Jun 2020 22:05:06: 4000000 INFO @ Sun, 21 Jun 2020 22:05:06: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:05:06: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:05:06: #1 total tags in treatment: 4006613 INFO @ Sun, 21 Jun 2020 22:05:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:05:06: #1 tags after filtering in treatment: 4006603 INFO @ Sun, 21 Jun 2020 22:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:06: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:07: #2 number of paired peaks: 1680 INFO @ Sun, 21 Jun 2020 22:05:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:07: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 22:05:07: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 22:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:07: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:07: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 22:05:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:05:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:05:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775921/SRX5775921.20_summits.bed INFO @ Sun, 21 Jun 2020 22:05:20: Done! pass1 - making usageList (437 chroms): 1 millis pass2 - checking and writing primary data (961 records, 4 fields): 13 millis CompletedMACS2peakCalling