Job ID = 6452758 SRX = SRX030962 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:38:22 prefetch.2.10.7: 1) Downloading 'SRR072390'... 2020-06-21T07:38:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:44:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:44:04 prefetch.2.10.7: 'SRR072390' is valid 2020-06-21T07:44:04 prefetch.2.10.7: 1) 'SRR072390' was downloaded successfully Read 22812818 spots for SRR072390/SRR072390.sra Written 22812818 spots for SRR072390/SRR072390.sra 2020-06-21T07:45:16 prefetch.2.10.7: 1) Downloading 'SRR072391'... 2020-06-21T07:45:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:45:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:45:31 prefetch.2.10.7: 'SRR072391' is valid 2020-06-21T07:45:31 prefetch.2.10.7: 1) 'SRR072391' was downloaded successfully Read 855422 spots for SRR072391/SRR072391.sra Written 855422 spots for SRR072391/SRR072391.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: 00:04:57 23668240 reads; of these: 23668240 (100.00%) were unpaired; of these: 6163203 (26.04%) aligned 0 times 10276249 (43.42%) aligned exactly 1 time 7228788 (30.54%) aligned >1 times 73.96% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 13825361 / 17505037 = 0.7898 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 16:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.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 16:53:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:45: 1000000 INFO @ Sun, 21 Jun 2020 16:53:52: 2000000 INFO @ Sun, 21 Jun 2020 16:53:59: 3000000 INFO @ Sun, 21 Jun 2020 16:54:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:04: #1 total tags in treatment: 3679676 INFO @ Sun, 21 Jun 2020 16:54:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:04: #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 16:54:04: #1 tags after filtering in treatment: 3679605 INFO @ Sun, 21 Jun 2020 16:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:04: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:04: #2 number of paired peaks: 2101 INFO @ Sun, 21 Jun 2020 16:54:04: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:05: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:05: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:05: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:05: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 16:54:05: #2 alternative fragment length(s) may be 3,37 bps INFO @ Sun, 21 Jun 2020 16:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.05_model.r WARNING @ Sun, 21 Jun 2020 16:54:05: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:54:05: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Sun, 21 Jun 2020 16:54:05: #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 16:54:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:05: #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 16:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.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 16:54:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:54:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:54:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:14: 1000000 INFO @ Sun, 21 Jun 2020 16:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.05_summits.bed INFO @ Sun, 21 Jun 2020 16:54:16: Done! pass1 - making usageList (552 chroms): 1 millis pass2 - checking and writing primary data (2844 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:54:19: 2000000 INFO @ Sun, 21 Jun 2020 16:54:25: 3000000 INFO @ Sun, 21 Jun 2020 16:54:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:29: #1 total tags in treatment: 3679676 INFO @ Sun, 21 Jun 2020 16:54:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:29: #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 16:54:29: #1 tags after filtering in treatment: 3679605 INFO @ Sun, 21 Jun 2020 16:54:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:29: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:29: #2 number of paired peaks: 2101 INFO @ Sun, 21 Jun 2020 16:54:29: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:30: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:30: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:30: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:30: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 16:54:30: #2 alternative fragment length(s) may be 3,37 bps INFO @ Sun, 21 Jun 2020 16:54:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.10_model.r WARNING @ Sun, 21 Jun 2020 16:54:30: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:54:30: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Sun, 21 Jun 2020 16:54:30: #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 16:54:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:30: #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 16:54:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.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 16:54:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:54:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.10_summits.bed INFO @ Sun, 21 Jun 2020 16:54:41: Done! pass1 - making usageList (495 chroms): 1 millis pass2 - checking and writing primary data (2550 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:54:44: 1000000 INFO @ Sun, 21 Jun 2020 16:54:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:54:55: 3000000 INFO @ Sun, 21 Jun 2020 16:54:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:54:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:54:59: #1 total tags in treatment: 3679676 INFO @ Sun, 21 Jun 2020 16:54:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:59: #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 16:55:00: #1 tags after filtering in treatment: 3679605 INFO @ Sun, 21 Jun 2020 16:55:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:55:00: #1 finished! INFO @ Sun, 21 Jun 2020 16:55:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:55:00: #2 number of paired peaks: 2101 INFO @ Sun, 21 Jun 2020 16:55:00: start model_add_line... INFO @ Sun, 21 Jun 2020 16:55:00: start X-correlation... INFO @ Sun, 21 Jun 2020 16:55:00: end of X-cor INFO @ Sun, 21 Jun 2020 16:55:00: #2 finished! INFO @ Sun, 21 Jun 2020 16:55:00: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 16:55:00: #2 alternative fragment length(s) may be 3,37 bps INFO @ Sun, 21 Jun 2020 16:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.20_model.r WARNING @ Sun, 21 Jun 2020 16:55:00: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:55:00: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Sun, 21 Jun 2020 16:55:00: #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 16:55:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:55:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:55:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX030962/SRX030962.20_summits.bed INFO @ Sun, 21 Jun 2020 16:55:11: Done! pass1 - making usageList (425 chroms): 1 millis pass2 - checking and writing primary data (1582 records, 4 fields): 15 millis CompletedMACS2peakCalling