Job ID = 6529422 SRX = SRX2618504 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:03:08 19131637 reads; of these: 19131637 (100.00%) were unpaired; of these: 5996860 (31.35%) aligned 0 times 12013841 (62.80%) aligned exactly 1 time 1120936 (5.86%) aligned >1 times 68.65% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 1032262 / 13134777 = 0.0786 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 @ Tue, 30 Jun 2020 02:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.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 @ Tue, 30 Jun 2020 02:04:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:33: 1000000 INFO @ Tue, 30 Jun 2020 02:04:38: 2000000 INFO @ Tue, 30 Jun 2020 02:04:43: 3000000 INFO @ Tue, 30 Jun 2020 02:04:48: 4000000 INFO @ Tue, 30 Jun 2020 02:04:53: 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 @ Tue, 30 Jun 2020 02:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.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 @ Tue, 30 Jun 2020 02:04:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:58: 6000000 INFO @ Tue, 30 Jun 2020 02:05:04: 1000000 INFO @ Tue, 30 Jun 2020 02:05:04: 7000000 INFO @ Tue, 30 Jun 2020 02:05:09: 2000000 INFO @ Tue, 30 Jun 2020 02:05:10: 8000000 INFO @ Tue, 30 Jun 2020 02:05:15: 3000000 INFO @ Tue, 30 Jun 2020 02:05:15: 9000000 INFO @ Tue, 30 Jun 2020 02:05:21: 4000000 INFO @ Tue, 30 Jun 2020 02:05:21: 10000000 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 @ Tue, 30 Jun 2020 02:05:27: 5000000 INFO @ Tue, 30 Jun 2020 02:05:27: 11000000 INFO @ Tue, 30 Jun 2020 02:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.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 @ Tue, 30 Jun 2020 02:05:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:32: 6000000 INFO @ Tue, 30 Jun 2020 02:05:33: 12000000 INFO @ Tue, 30 Jun 2020 02:05:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:05:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:05:34: #1 total tags in treatment: 12102515 INFO @ Tue, 30 Jun 2020 02:05:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:05:34: #1 tags after filtering in treatment: 12102423 INFO @ Tue, 30 Jun 2020 02:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:34: 1000000 INFO @ Tue, 30 Jun 2020 02:05:35: #2 number of paired peaks: 138 WARNING @ Tue, 30 Jun 2020 02:05:35: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:35: #2 predicted fragment length is 132 bps INFO @ Tue, 30 Jun 2020 02:05:35: #2 alternative fragment length(s) may be 4,82,108,132,144 bps INFO @ Tue, 30 Jun 2020 02:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.05_model.r INFO @ Tue, 30 Jun 2020 02:05:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:38: 7000000 INFO @ Tue, 30 Jun 2020 02:05:40: 2000000 INFO @ Tue, 30 Jun 2020 02:05:44: 8000000 INFO @ Tue, 30 Jun 2020 02:05:46: 3000000 INFO @ Tue, 30 Jun 2020 02:05:49: 9000000 INFO @ Tue, 30 Jun 2020 02:05:52: 4000000 INFO @ Tue, 30 Jun 2020 02:05:55: 10000000 INFO @ Tue, 30 Jun 2020 02:05:57: 5000000 INFO @ Tue, 30 Jun 2020 02:06:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:01: 11000000 INFO @ Tue, 30 Jun 2020 02:06:03: 6000000 INFO @ Tue, 30 Jun 2020 02:06:06: 12000000 INFO @ Tue, 30 Jun 2020 02:06:07: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:07: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:07: #1 total tags in treatment: 12102515 INFO @ Tue, 30 Jun 2020 02:06:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:06:08: #1 tags after filtering in treatment: 12102423 INFO @ Tue, 30 Jun 2020 02:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:08: #2 number of paired peaks: 138 WARNING @ Tue, 30 Jun 2020 02:06:08: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:08: #2 predicted fragment length is 132 bps INFO @ Tue, 30 Jun 2020 02:06:08: #2 alternative fragment length(s) may be 4,82,108,132,144 bps INFO @ Tue, 30 Jun 2020 02:06:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.10_model.r INFO @ Tue, 30 Jun 2020 02:06:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:08: 7000000 INFO @ Tue, 30 Jun 2020 02:06:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.05_summits.bed INFO @ Tue, 30 Jun 2020 02:06:12: Done! pass1 - making usageList (157 chroms): 1 millis pass2 - checking and writing primary data (1299 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:06:14: 8000000 INFO @ Tue, 30 Jun 2020 02:06:19: 9000000 INFO @ Tue, 30 Jun 2020 02:06:25: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:06:30: 11000000 INFO @ Tue, 30 Jun 2020 02:06:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:35: 12000000 INFO @ Tue, 30 Jun 2020 02:06:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:35: #1 total tags in treatment: 12102515 INFO @ Tue, 30 Jun 2020 02:06:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:06:36: #1 tags after filtering in treatment: 12102423 INFO @ Tue, 30 Jun 2020 02:06:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:37: #2 number of paired peaks: 138 WARNING @ Tue, 30 Jun 2020 02:06:37: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:37: #2 predicted fragment length is 132 bps INFO @ Tue, 30 Jun 2020 02:06:37: #2 alternative fragment length(s) may be 4,82,108,132,144 bps INFO @ Tue, 30 Jun 2020 02:06:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.20_model.r INFO @ Tue, 30 Jun 2020 02:06:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.10_summits.bed INFO @ Tue, 30 Jun 2020 02:06:45: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:07:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618504/SRX2618504.20_summits.bed INFO @ Tue, 30 Jun 2020 02:07:12: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 3 millis CompletedMACS2peakCalling