Job ID = 6529721 SRX = SRX4375871 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: 00:05:32 22261061 reads; of these: 22261061 (100.00%) were unpaired; of these: 1893128 (8.50%) aligned 0 times 15573730 (69.96%) aligned exactly 1 time 4794203 (21.54%) aligned >1 times 91.50% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 3948371 / 20367933 = 0.1939 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 03:04:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.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 03:04:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:04:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:04:37: 1000000 INFO @ Tue, 30 Jun 2020 03:04:45: 2000000 INFO @ Tue, 30 Jun 2020 03:04:53: 3000000 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 03:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.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 03:04:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:04:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:05:01: 4000000 INFO @ Tue, 30 Jun 2020 03:05:07: 1000000 INFO @ Tue, 30 Jun 2020 03:05:09: 5000000 INFO @ Tue, 30 Jun 2020 03:05:15: 2000000 INFO @ Tue, 30 Jun 2020 03:05:17: 6000000 INFO @ Tue, 30 Jun 2020 03:05:23: 3000000 INFO @ Tue, 30 Jun 2020 03:05:26: 7000000 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 03:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.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 03:05:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:05:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:05:31: 4000000 INFO @ Tue, 30 Jun 2020 03:05:34: 8000000 INFO @ Tue, 30 Jun 2020 03:05:38: 1000000 INFO @ Tue, 30 Jun 2020 03:05:39: 5000000 INFO @ Tue, 30 Jun 2020 03:05:43: 9000000 INFO @ Tue, 30 Jun 2020 03:05:46: 2000000 INFO @ Tue, 30 Jun 2020 03:05:48: 6000000 INFO @ Tue, 30 Jun 2020 03:05:51: 10000000 INFO @ Tue, 30 Jun 2020 03:05:55: 3000000 INFO @ Tue, 30 Jun 2020 03:05:56: 7000000 INFO @ Tue, 30 Jun 2020 03:06:00: 11000000 INFO @ Tue, 30 Jun 2020 03:06:05: 4000000 INFO @ Tue, 30 Jun 2020 03:06:05: 8000000 INFO @ Tue, 30 Jun 2020 03:06:08: 12000000 INFO @ Tue, 30 Jun 2020 03:06:14: 9000000 INFO @ Tue, 30 Jun 2020 03:06:14: 5000000 INFO @ Tue, 30 Jun 2020 03:06:18: 13000000 INFO @ Tue, 30 Jun 2020 03:06:22: 10000000 INFO @ Tue, 30 Jun 2020 03:06:23: 6000000 INFO @ Tue, 30 Jun 2020 03:06:26: 14000000 INFO @ Tue, 30 Jun 2020 03:06:30: 11000000 INFO @ Tue, 30 Jun 2020 03:06:32: 7000000 INFO @ Tue, 30 Jun 2020 03:06:34: 15000000 INFO @ Tue, 30 Jun 2020 03:06:39: 12000000 INFO @ Tue, 30 Jun 2020 03:06:42: 8000000 INFO @ Tue, 30 Jun 2020 03:06:44: 16000000 INFO @ Tue, 30 Jun 2020 03:06:48: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:06:48: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:06:48: #1 total tags in treatment: 16419562 INFO @ Tue, 30 Jun 2020 03:06:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:06:48: #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 03:06:48: 13000000 INFO @ Tue, 30 Jun 2020 03:06:48: #1 tags after filtering in treatment: 16419468 INFO @ Tue, 30 Jun 2020 03:06:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:06:48: #1 finished! INFO @ Tue, 30 Jun 2020 03:06:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:06:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:06:49: #2 number of paired peaks: 717 WARNING @ Tue, 30 Jun 2020 03:06:49: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Tue, 30 Jun 2020 03:06:49: start model_add_line... INFO @ Tue, 30 Jun 2020 03:06:50: start X-correlation... INFO @ Tue, 30 Jun 2020 03:06:50: end of X-cor INFO @ Tue, 30 Jun 2020 03:06:50: #2 finished! INFO @ Tue, 30 Jun 2020 03:06:50: #2 predicted fragment length is 171 bps INFO @ Tue, 30 Jun 2020 03:06:50: #2 alternative fragment length(s) may be 4,171 bps INFO @ Tue, 30 Jun 2020 03:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.05_model.r INFO @ Tue, 30 Jun 2020 03:06:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:06:51: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:06:56: 14000000 INFO @ Tue, 30 Jun 2020 03:07:01: 10000000 INFO @ Tue, 30 Jun 2020 03:07:04: 15000000 INFO @ Tue, 30 Jun 2020 03:07:10: 11000000 INFO @ Tue, 30 Jun 2020 03:07:13: 16000000 INFO @ Tue, 30 Jun 2020 03:07:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:07:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:07:17: #1 total tags in treatment: 16419562 INFO @ Tue, 30 Jun 2020 03:07:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:07:17: #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 03:07:17: #1 tags after filtering in treatment: 16419468 INFO @ Tue, 30 Jun 2020 03:07:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:07:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:07:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:07:19: #2 number of paired peaks: 717 WARNING @ Tue, 30 Jun 2020 03:07:19: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Tue, 30 Jun 2020 03:07:19: start model_add_line... INFO @ Tue, 30 Jun 2020 03:07:19: start X-correlation... INFO @ Tue, 30 Jun 2020 03:07:19: end of X-cor INFO @ Tue, 30 Jun 2020 03:07:19: #2 finished! INFO @ Tue, 30 Jun 2020 03:07:19: #2 predicted fragment length is 171 bps INFO @ Tue, 30 Jun 2020 03:07:19: #2 alternative fragment length(s) may be 4,171 bps INFO @ Tue, 30 Jun 2020 03:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.10_model.r INFO @ Tue, 30 Jun 2020 03:07:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:07:20: 12000000 INFO @ Tue, 30 Jun 2020 03:07:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:07:30: 13000000 INFO @ Tue, 30 Jun 2020 03:07:39: 14000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.05_summits.bed INFO @ Tue, 30 Jun 2020 03:07:43: Done! pass1 - making usageList (730 chroms): 4 millis pass2 - checking and writing primary data (15301 records, 4 fields): 68 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:07:49: 15000000 INFO @ Tue, 30 Jun 2020 03:07:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:07:59: 16000000 INFO @ Tue, 30 Jun 2020 03:08:03: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:08:03: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:08:03: #1 total tags in treatment: 16419562 INFO @ Tue, 30 Jun 2020 03:08:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:08:03: #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 03:08:04: #1 tags after filtering in treatment: 16419468 INFO @ Tue, 30 Jun 2020 03:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:08:04: #1 finished! INFO @ Tue, 30 Jun 2020 03:08:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:08:05: #2 number of paired peaks: 717 WARNING @ Tue, 30 Jun 2020 03:08:05: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Tue, 30 Jun 2020 03:08:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:08:05: start X-correlation... INFO @ Tue, 30 Jun 2020 03:08:05: end of X-cor INFO @ Tue, 30 Jun 2020 03:08:05: #2 finished! INFO @ Tue, 30 Jun 2020 03:08:05: #2 predicted fragment length is 171 bps INFO @ Tue, 30 Jun 2020 03:08:05: #2 alternative fragment length(s) may be 4,171 bps INFO @ Tue, 30 Jun 2020 03:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.20_model.r INFO @ Tue, 30 Jun 2020 03:08:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:08:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.10_summits.bed INFO @ Tue, 30 Jun 2020 03:08:12: Done! pass1 - making usageList (600 chroms): 3 millis pass2 - checking and writing primary data (5496 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:08:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:08:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375871/SRX4375871.20_summits.bed INFO @ Tue, 30 Jun 2020 03:08:58: Done! pass1 - making usageList (399 chroms): 2 millis pass2 - checking and writing primary data (1476 records, 4 fields): 23 millis CompletedMACS2peakCalling