Job ID = 6453363 SRX = SRX1120695 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:21:47 prefetch.2.10.7: 1) Downloading 'SRR2129927'... 2020-06-21T08:21:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:21 prefetch.2.10.7: 1) 'SRR2129927' was downloaded successfully Read 16190572 spots for SRR2129927/SRR2129927.sra Written 16190572 spots for SRR2129927/SRR2129927.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: 00:05:51 16190572 reads; of these: 16190572 (100.00%) were unpaired; of these: 5567239 (34.39%) aligned 0 times 4381979 (27.07%) aligned exactly 1 time 6241354 (38.55%) aligned >1 times 65.61% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 6192383 / 10623333 = 0.5829 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 17:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.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 17:34:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:16: 1000000 INFO @ Sun, 21 Jun 2020 17:34:21: 2000000 INFO @ Sun, 21 Jun 2020 17:34:27: 3000000 INFO @ Sun, 21 Jun 2020 17:34:32: 4000000 INFO @ Sun, 21 Jun 2020 17:34:35: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:34:35: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:34:35: #1 total tags in treatment: 4430950 INFO @ Sun, 21 Jun 2020 17:34:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:35: #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 17:34:35: #1 tags after filtering in treatment: 4430874 INFO @ Sun, 21 Jun 2020 17:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:36: #2 number of paired peaks: 7427 INFO @ Sun, 21 Jun 2020 17:34:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:36: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 17:34:36: #2 alternative fragment length(s) may be 3,96 bps INFO @ Sun, 21 Jun 2020 17:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.05_model.r WARNING @ Sun, 21 Jun 2020 17:34:36: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:34:36: #2 You may need to consider one of the other alternative d(s): 3,96 WARNING @ Sun, 21 Jun 2020 17:34:36: #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 17:34:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:36: #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 17:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.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 17:34:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:46: 1000000 INFO @ Sun, 21 Jun 2020 17:34:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.05_summits.bed INFO @ Sun, 21 Jun 2020 17:34:51: Done! pass1 - making usageList (1014 chroms): 1 millis pass2 - checking and writing primary data (3965 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:34:52: 2000000 INFO @ Sun, 21 Jun 2020 17:34:57: 3000000 INFO @ Sun, 21 Jun 2020 17:35:03: 4000000 INFO @ Sun, 21 Jun 2020 17:35:05: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:35:05: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:35:05: #1 total tags in treatment: 4430950 INFO @ Sun, 21 Jun 2020 17:35:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:05: #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 17:35:05: #1 tags after filtering in treatment: 4430874 INFO @ Sun, 21 Jun 2020 17:35:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:06: #2 number of paired peaks: 7427 INFO @ Sun, 21 Jun 2020 17:35:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:06: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 17:35:06: #2 alternative fragment length(s) may be 3,96 bps INFO @ Sun, 21 Jun 2020 17:35:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.10_model.r WARNING @ Sun, 21 Jun 2020 17:35:06: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:35:06: #2 You may need to consider one of the other alternative d(s): 3,96 WARNING @ Sun, 21 Jun 2020 17:35:06: #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 17:35:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:06: #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 17:35:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.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 17:35:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:35:16: 1000000 INFO @ Sun, 21 Jun 2020 17:35:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:35:21: 2000000 INFO @ Sun, 21 Jun 2020 17:35:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.10_summits.bed INFO @ Sun, 21 Jun 2020 17:35:21: Done! pass1 - making usageList (751 chroms): 1 millis pass2 - checking and writing primary data (2069 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:35:27: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:35:32: 4000000 INFO @ Sun, 21 Jun 2020 17:35:35: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:35:35: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:35:35: #1 total tags in treatment: 4430950 INFO @ Sun, 21 Jun 2020 17:35:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:35: #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 17:35:35: #1 tags after filtering in treatment: 4430874 INFO @ Sun, 21 Jun 2020 17:35:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:36: #2 number of paired peaks: 7427 INFO @ Sun, 21 Jun 2020 17:35:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:36: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 17:35:36: #2 alternative fragment length(s) may be 3,96 bps INFO @ Sun, 21 Jun 2020 17:35:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.20_model.r WARNING @ Sun, 21 Jun 2020 17:35:36: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:35:36: #2 You may need to consider one of the other alternative d(s): 3,96 WARNING @ Sun, 21 Jun 2020 17:35:36: #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 17:35:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:35:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:35:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120695/SRX1120695.20_summits.bed INFO @ Sun, 21 Jun 2020 17:35:52: Done! pass1 - making usageList (530 chroms): 1 millis pass2 - checking and writing primary data (1148 records, 4 fields): 16 millis CompletedMACS2peakCalling