Job ID = 6456125 SRX = SRX318798 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:37:29 prefetch.2.10.7: 1) Downloading 'SRR927114'... 2020-06-21T10:37:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:22 prefetch.2.10.7: 1) 'SRR927114' was downloaded successfully Read 18127616 spots for SRR927114/SRR927114.sra Written 18127616 spots for SRR927114/SRR927114.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: 00:05:36 18127616 reads; of these: 18127616 (100.00%) were unpaired; of these: 1064702 (5.87%) aligned 0 times 10988574 (60.62%) aligned exactly 1 time 6074340 (33.51%) aligned >1 times 94.13% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 3492806 / 17062914 = 0.2047 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 19:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.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 19:51:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:31: 1000000 INFO @ Sun, 21 Jun 2020 19:51:38: 2000000 INFO @ Sun, 21 Jun 2020 19:51:44: 3000000 INFO @ Sun, 21 Jun 2020 19:51:50: 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 19:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.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 19:51:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:57: 5000000 INFO @ Sun, 21 Jun 2020 19:52:01: 1000000 INFO @ Sun, 21 Jun 2020 19:52:03: 6000000 INFO @ Sun, 21 Jun 2020 19:52:08: 2000000 INFO @ Sun, 21 Jun 2020 19:52:09: 7000000 INFO @ Sun, 21 Jun 2020 19:52:15: 3000000 INFO @ Sun, 21 Jun 2020 19:52:16: 8000000 INFO @ Sun, 21 Jun 2020 19:52:21: 4000000 INFO @ Sun, 21 Jun 2020 19:52:22: 9000000 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 19:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.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 19:52:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:28: 5000000 INFO @ Sun, 21 Jun 2020 19:52:29: 10000000 INFO @ Sun, 21 Jun 2020 19:52:31: 1000000 INFO @ Sun, 21 Jun 2020 19:52:34: 6000000 INFO @ Sun, 21 Jun 2020 19:52:35: 11000000 INFO @ Sun, 21 Jun 2020 19:52:37: 2000000 INFO @ Sun, 21 Jun 2020 19:52:41: 7000000 INFO @ Sun, 21 Jun 2020 19:52:42: 12000000 INFO @ Sun, 21 Jun 2020 19:52:43: 3000000 INFO @ Sun, 21 Jun 2020 19:52:48: 8000000 INFO @ Sun, 21 Jun 2020 19:52:49: 13000000 INFO @ Sun, 21 Jun 2020 19:52:49: 4000000 INFO @ Sun, 21 Jun 2020 19:52:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:52:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:52:52: #1 total tags in treatment: 13570108 INFO @ Sun, 21 Jun 2020 19:52:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:52: #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 19:52:53: #1 tags after filtering in treatment: 13570108 INFO @ Sun, 21 Jun 2020 19:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:54: #2 number of paired peaks: 1119 INFO @ Sun, 21 Jun 2020 19:52:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:54: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:52:54: #2 alternative fragment length(s) may be 2,47,546 bps INFO @ Sun, 21 Jun 2020 19:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.05_model.r WARNING @ Sun, 21 Jun 2020 19:52:54: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:52:54: #2 You may need to consider one of the other alternative d(s): 2,47,546 WARNING @ Sun, 21 Jun 2020 19:52:54: #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 19:52:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:52:54: 9000000 INFO @ Sun, 21 Jun 2020 19:52:55: 5000000 INFO @ Sun, 21 Jun 2020 19:53:01: 6000000 INFO @ Sun, 21 Jun 2020 19:53:01: 10000000 INFO @ Sun, 21 Jun 2020 19:53:07: 7000000 INFO @ Sun, 21 Jun 2020 19:53:07: 11000000 INFO @ Sun, 21 Jun 2020 19:53:13: 8000000 INFO @ Sun, 21 Jun 2020 19:53:14: 12000000 INFO @ Sun, 21 Jun 2020 19:53:19: 9000000 INFO @ Sun, 21 Jun 2020 19:53:21: 13000000 INFO @ Sun, 21 Jun 2020 19:53:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:24: 10000000 INFO @ Sun, 21 Jun 2020 19:53:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:53:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:53:25: #1 total tags in treatment: 13570108 INFO @ Sun, 21 Jun 2020 19:53:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:25: #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 19:53:25: #1 tags after filtering in treatment: 13570108 INFO @ Sun, 21 Jun 2020 19:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:26: #2 number of paired peaks: 1119 INFO @ Sun, 21 Jun 2020 19:53:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:26: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:53:26: #2 alternative fragment length(s) may be 2,47,546 bps INFO @ Sun, 21 Jun 2020 19:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.10_model.r WARNING @ Sun, 21 Jun 2020 19:53:26: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:53:26: #2 You may need to consider one of the other alternative d(s): 2,47,546 WARNING @ Sun, 21 Jun 2020 19:53:26: #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 19:53:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:30: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:53:36: 12000000 INFO @ Sun, 21 Jun 2020 19:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.05_summits.bed INFO @ Sun, 21 Jun 2020 19:53:38: Done! pass1 - making usageList (657 chroms): 2 millis pass2 - checking and writing primary data (2933 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:53:41: 13000000 INFO @ Sun, 21 Jun 2020 19:53:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:53:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:53:45: #1 total tags in treatment: 13570108 INFO @ Sun, 21 Jun 2020 19:53:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:45: #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 19:53:45: #1 tags after filtering in treatment: 13570108 INFO @ Sun, 21 Jun 2020 19:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:46: #2 number of paired peaks: 1119 INFO @ Sun, 21 Jun 2020 19:53:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:46: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:53:46: #2 alternative fragment length(s) may be 2,47,546 bps INFO @ Sun, 21 Jun 2020 19:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.20_model.r WARNING @ Sun, 21 Jun 2020 19:53:46: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:53:46: #2 You may need to consider one of the other alternative d(s): 2,47,546 WARNING @ Sun, 21 Jun 2020 19:53:46: #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 19:53:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.10_summits.bed INFO @ Sun, 21 Jun 2020 19:54:09: Done! pass1 - making usageList (564 chroms): 1 millis pass2 - checking and writing primary data (2266 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:54:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318798/SRX318798.20_summits.bed INFO @ Sun, 21 Jun 2020 19:54:28: Done! pass1 - making usageList (397 chroms): 1 millis pass2 - checking and writing primary data (954 records, 4 fields): 14 millis CompletedMACS2peakCalling