Job ID = 6453811 SRX = SRX149197 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:33:54 prefetch.2.10.7: 1) Downloading 'SRR500157'... 2020-06-21T08:33:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:39:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:39:36 prefetch.2.10.7: 1) 'SRR500157' was downloaded successfully Read 28251307 spots for SRR500157/SRR500157.sra Written 28251307 spots for SRR500157/SRR500157.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: 00:06:01 28251307 reads; of these: 28251307 (100.00%) were unpaired; of these: 8350219 (29.56%) aligned 0 times 13360624 (47.29%) aligned exactly 1 time 6540464 (23.15%) aligned >1 times 70.44% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 11040630 / 19901088 = 0.5548 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 17:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.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 17:50:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:49: 1000000 INFO @ Sun, 21 Jun 2020 17:50:54: 2000000 INFO @ Sun, 21 Jun 2020 17:51:00: 3000000 INFO @ Sun, 21 Jun 2020 17:51:05: 4000000 INFO @ Sun, 21 Jun 2020 17:51:10: 5000000 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 17:51:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.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 17:51:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:16: 6000000 INFO @ Sun, 21 Jun 2020 17:51:19: 1000000 INFO @ Sun, 21 Jun 2020 17:51:22: 7000000 INFO @ Sun, 21 Jun 2020 17:51:25: 2000000 INFO @ Sun, 21 Jun 2020 17:51:28: 8000000 INFO @ Sun, 21 Jun 2020 17:51:32: 3000000 INFO @ Sun, 21 Jun 2020 17:51:34: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:51:34: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:51:34: #1 total tags in treatment: 8860458 INFO @ Sun, 21 Jun 2020 17:51:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:34: #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 17:51:34: #1 tags after filtering in treatment: 8860388 INFO @ Sun, 21 Jun 2020 17:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:35: #2 number of paired peaks: 3423 INFO @ Sun, 21 Jun 2020 17:51:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:35: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 17:51:35: #2 alternative fragment length(s) may be 2,40 bps INFO @ Sun, 21 Jun 2020 17:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.05_model.r WARNING @ Sun, 21 Jun 2020 17:51:35: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:51:35: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Sun, 21 Jun 2020 17:51:35: #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 17:51:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:51:37: 4000000 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 17:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.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 17:51:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:43: 5000000 INFO @ Sun, 21 Jun 2020 17:51:49: 1000000 INFO @ Sun, 21 Jun 2020 17:51:49: 6000000 INFO @ Sun, 21 Jun 2020 17:51:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:55: 2000000 INFO @ Sun, 21 Jun 2020 17:51:55: 7000000 INFO @ Sun, 21 Jun 2020 17:52:01: 3000000 INFO @ Sun, 21 Jun 2020 17:52:02: 8000000 INFO @ Sun, 21 Jun 2020 17:52:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.05_summits.bed INFO @ Sun, 21 Jun 2020 17:52:02: Done! pass1 - making usageList (764 chroms): 2 millis pass2 - checking and writing primary data (3952 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:07: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:52:07: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:52:07: #1 total tags in treatment: 8860458 INFO @ Sun, 21 Jun 2020 17:52:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:07: #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 17:52:07: 4000000 INFO @ Sun, 21 Jun 2020 17:52:07: #1 tags after filtering in treatment: 8860388 INFO @ Sun, 21 Jun 2020 17:52:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:07: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:08: #2 number of paired peaks: 3423 INFO @ Sun, 21 Jun 2020 17:52:08: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:08: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:08: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:08: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:08: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 17:52:08: #2 alternative fragment length(s) may be 2,40 bps INFO @ Sun, 21 Jun 2020 17:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.10_model.r WARNING @ Sun, 21 Jun 2020 17:52:08: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:08: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Sun, 21 Jun 2020 17:52:08: #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 17:52:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:13: 5000000 INFO @ Sun, 21 Jun 2020 17:52:18: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:52:24: 7000000 INFO @ Sun, 21 Jun 2020 17:52:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:30: 8000000 INFO @ Sun, 21 Jun 2020 17:52:35: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:52:35: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:52:35: #1 total tags in treatment: 8860458 INFO @ Sun, 21 Jun 2020 17:52:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:35: #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 17:52:35: #1 tags after filtering in treatment: 8860388 INFO @ Sun, 21 Jun 2020 17:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:36: #2 number of paired peaks: 3423 INFO @ Sun, 21 Jun 2020 17:52:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:36: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 17:52:36: #2 alternative fragment length(s) may be 2,40 bps INFO @ Sun, 21 Jun 2020 17:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.20_model.r WARNING @ Sun, 21 Jun 2020 17:52:36: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:36: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Sun, 21 Jun 2020 17:52:36: #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 17:52:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.10_summits.bed INFO @ Sun, 21 Jun 2020 17:52:36: Done! pass1 - making usageList (589 chroms): 1 millis pass2 - checking and writing primary data (2563 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:52:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149197/SRX149197.20_summits.bed INFO @ Sun, 21 Jun 2020 17:53:03: Done! pass1 - making usageList (323 chroms): 1 millis pass2 - checking and writing primary data (783 records, 4 fields): 10 millis CompletedMACS2peakCalling