Job ID = 6456581 SRX = SRX365699 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:09:09 prefetch.2.10.7: 1) Downloading 'SRR1013777'... 2020-06-21T11:09:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:14 prefetch.2.10.7: 1) 'SRR1013777' was downloaded successfully Read 29791523 spots for SRR1013777/SRR1013777.sra Written 29791523 spots for SRR1013777/SRR1013777.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: 00:06:50 29791523 reads; of these: 29791523 (100.00%) were unpaired; of these: 8072044 (27.10%) aligned 0 times 16344996 (54.86%) aligned exactly 1 time 5374483 (18.04%) aligned >1 times 72.90% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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 12 files... [bam_rmdupse_core] 13951817 / 21719479 = 0.6424 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 20:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.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 20:28:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:18: 1000000 INFO @ Sun, 21 Jun 2020 20:28:24: 2000000 INFO @ Sun, 21 Jun 2020 20:28:29: 3000000 INFO @ Sun, 21 Jun 2020 20:28:35: 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 @ Sun, 21 Jun 2020 20:28:41: 5000000 INFO @ Sun, 21 Jun 2020 20:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.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 20:28:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:49: 6000000 INFO @ Sun, 21 Jun 2020 20:28:50: 1000000 INFO @ Sun, 21 Jun 2020 20:28:56: 7000000 INFO @ Sun, 21 Jun 2020 20:28:57: 2000000 INFO @ Sun, 21 Jun 2020 20:29:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:02: #1 total tags in treatment: 7767662 INFO @ Sun, 21 Jun 2020 20:29:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:02: #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 20:29:02: #1 tags after filtering in treatment: 7767586 INFO @ Sun, 21 Jun 2020 20:29:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:03: #2 number of paired peaks: 2734 INFO @ Sun, 21 Jun 2020 20:29:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:03: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 20:29:03: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 20:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.05_model.r WARNING @ Sun, 21 Jun 2020 20:29:03: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:29:03: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 20:29:03: #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 20:29:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:05: 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 @ Sun, 21 Jun 2020 20:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.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 20:29:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:12: 4000000 INFO @ Sun, 21 Jun 2020 20:29:19: 1000000 INFO @ Sun, 21 Jun 2020 20:29:20: 5000000 INFO @ Sun, 21 Jun 2020 20:29:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:26: 2000000 INFO @ Sun, 21 Jun 2020 20:29:28: 6000000 INFO @ Sun, 21 Jun 2020 20:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.05_summits.bed INFO @ Sun, 21 Jun 2020 20:29:30: Done! pass1 - making usageList (815 chroms): 2 millis pass2 - checking and writing primary data (5498 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:29:33: 3000000 INFO @ Sun, 21 Jun 2020 20:29:36: 7000000 INFO @ Sun, 21 Jun 2020 20:29:39: 4000000 INFO @ Sun, 21 Jun 2020 20:29:42: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:42: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:42: #1 total tags in treatment: 7767662 INFO @ Sun, 21 Jun 2020 20:29:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:42: #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 20:29:42: #1 tags after filtering in treatment: 7767586 INFO @ Sun, 21 Jun 2020 20:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:43: #2 number of paired peaks: 2734 INFO @ Sun, 21 Jun 2020 20:29:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:43: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 20:29:43: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 20:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.10_model.r WARNING @ Sun, 21 Jun 2020 20:29:43: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:29:43: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 20:29:43: #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 20:29:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:46: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:29:52: 6000000 INFO @ Sun, 21 Jun 2020 20:29:58: 7000000 INFO @ Sun, 21 Jun 2020 20:30:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:30:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:30:03: #1 total tags in treatment: 7767662 INFO @ Sun, 21 Jun 2020 20:30:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:30:03: #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 20:30:03: #1 tags after filtering in treatment: 7767586 INFO @ Sun, 21 Jun 2020 20:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:03: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:30:04: #2 number of paired peaks: 2734 INFO @ Sun, 21 Jun 2020 20:30:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:30:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:30:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:04: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 20:30:04: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 20:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.20_model.r WARNING @ Sun, 21 Jun 2020 20:30:04: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:30:04: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 20:30:04: #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 20:30:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.10_summits.bed INFO @ Sun, 21 Jun 2020 20:30:09: Done! pass1 - making usageList (690 chroms): 2 millis pass2 - checking and writing primary data (3583 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:30:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365699/SRX365699.20_summits.bed INFO @ Sun, 21 Jun 2020 20:30:31: Done! pass1 - making usageList (502 chroms): 2 millis pass2 - checking and writing primary data (2374 records, 4 fields): 16 millis CompletedMACS2peakCalling