Job ID = 6456291 SRX = SRX335496 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:45:39 prefetch.2.10.7: 1) Downloading 'SRR952838'... 2020-06-21T10:45:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:50:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:50:04 prefetch.2.10.7: 1) 'SRR952838' was downloaded successfully Read 16173126 spots for SRR952838/SRR952838.sra Written 16173126 spots for SRR952838/SRR952838.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:26 16173126 reads; of these: 16173126 (100.00%) were unpaired; of these: 7357766 (45.49%) aligned 0 times 4436398 (27.43%) aligned exactly 1 time 4378962 (27.08%) aligned >1 times 54.51% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 4628360 / 8815360 = 0.5250 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 19:57:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.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 19:57:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:33: 1000000 INFO @ Sun, 21 Jun 2020 19:57:39: 2000000 INFO @ Sun, 21 Jun 2020 19:57:45: 3000000 INFO @ Sun, 21 Jun 2020 19:57:51: 4000000 INFO @ Sun, 21 Jun 2020 19:57:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:57:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:57:52: #1 total tags in treatment: 4187000 INFO @ Sun, 21 Jun 2020 19:57:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:52: #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 19:57:52: #1 tags after filtering in treatment: 4186838 INFO @ Sun, 21 Jun 2020 19:57:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:53: #2 number of paired peaks: 2942 INFO @ Sun, 21 Jun 2020 19:57:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:53: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:57:53: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 19:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.05_model.r WARNING @ Sun, 21 Jun 2020 19:57:53: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:53: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 21 Jun 2020 19:57:53: #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 19:57:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:53: #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 19:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.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 19:57:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:04: 1000000 INFO @ Sun, 21 Jun 2020 19:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.05_summits.bed INFO @ Sun, 21 Jun 2020 19:58:06: Done! pass1 - making usageList (692 chroms): 1 millis pass2 - checking and writing primary data (2591 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:58:10: 2000000 INFO @ Sun, 21 Jun 2020 19:58:15: 3000000 INFO @ Sun, 21 Jun 2020 19:58:21: 4000000 INFO @ Sun, 21 Jun 2020 19:58:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:58:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:58:22: #1 total tags in treatment: 4187000 INFO @ Sun, 21 Jun 2020 19:58:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:22: #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 19:58:22: #1 tags after filtering in treatment: 4186838 INFO @ Sun, 21 Jun 2020 19:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:23: #2 number of paired peaks: 2942 INFO @ Sun, 21 Jun 2020 19:58:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:23: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:58:23: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 19:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.10_model.r WARNING @ Sun, 21 Jun 2020 19:58:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:58:23: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 21 Jun 2020 19:58:23: #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 19:58:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:23: #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 19:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.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 19:58:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:34: 1000000 INFO @ Sun, 21 Jun 2020 19:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.10_summits.bed INFO @ Sun, 21 Jun 2020 19:58:36: Done! pass1 - making usageList (548 chroms): 2 millis pass2 - checking and writing primary data (1870 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:58:39: 2000000 INFO @ Sun, 21 Jun 2020 19:58:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:58:51: 4000000 INFO @ Sun, 21 Jun 2020 19:58:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:58:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:58:52: #1 total tags in treatment: 4187000 INFO @ Sun, 21 Jun 2020 19:58:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:52: #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 19:58:52: #1 tags after filtering in treatment: 4186838 INFO @ Sun, 21 Jun 2020 19:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:53: #2 number of paired peaks: 2942 INFO @ Sun, 21 Jun 2020 19:58:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:53: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:58:53: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 21 Jun 2020 19:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.20_model.r WARNING @ Sun, 21 Jun 2020 19:58:53: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:58:53: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 21 Jun 2020 19:58:53: #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 19:58:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:59:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335496/SRX335496.20_summits.bed INFO @ Sun, 21 Jun 2020 19:59:06: Done! pass1 - making usageList (355 chroms): 1 millis pass2 - checking and writing primary data (855 records, 4 fields): 11 millis CompletedMACS2peakCalling