Job ID = 6529209 SRX = SRX042244 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: 00:07:29 19158137 reads; of these: 19158137 (100.00%) were unpaired; of these: 4531820 (23.65%) aligned 0 times 11954363 (62.40%) aligned exactly 1 time 2671954 (13.95%) aligned >1 times 76.35% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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] 4497249 / 14626317 = 0.3075 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 01:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.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 01:44:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:44:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:44:20: 1000000 INFO @ Tue, 30 Jun 2020 01:44:26: 2000000 INFO @ Tue, 30 Jun 2020 01:44:33: 3000000 INFO @ Tue, 30 Jun 2020 01:44:40: 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 @ Tue, 30 Jun 2020 01:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.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 01:44:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:44:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:44:47: 5000000 INFO @ Tue, 30 Jun 2020 01:44:51: 1000000 INFO @ Tue, 30 Jun 2020 01:44:54: 6000000 INFO @ Tue, 30 Jun 2020 01:44:59: 2000000 INFO @ Tue, 30 Jun 2020 01:45:01: 7000000 INFO @ Tue, 30 Jun 2020 01:45:06: 3000000 INFO @ Tue, 30 Jun 2020 01:45:09: 8000000 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 01:45:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.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 01:45:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:14: 4000000 INFO @ Tue, 30 Jun 2020 01:45:17: 9000000 INFO @ Tue, 30 Jun 2020 01:45:22: 1000000 INFO @ Tue, 30 Jun 2020 01:45:22: 5000000 INFO @ Tue, 30 Jun 2020 01:45:25: 10000000 INFO @ Tue, 30 Jun 2020 01:45:26: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 01:45:26: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 01:45:26: #1 total tags in treatment: 10129068 INFO @ Tue, 30 Jun 2020 01:45:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:45:26: #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 01:45:27: #1 tags after filtering in treatment: 10129035 INFO @ Tue, 30 Jun 2020 01:45:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:45:27: #1 finished! INFO @ Tue, 30 Jun 2020 01:45:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:45:28: #2 number of paired peaks: 182 WARNING @ Tue, 30 Jun 2020 01:45:28: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 30 Jun 2020 01:45:28: start model_add_line... INFO @ Tue, 30 Jun 2020 01:45:28: start X-correlation... INFO @ Tue, 30 Jun 2020 01:45:28: end of X-cor INFO @ Tue, 30 Jun 2020 01:45:28: #2 finished! INFO @ Tue, 30 Jun 2020 01:45:28: #2 predicted fragment length is 332 bps INFO @ Tue, 30 Jun 2020 01:45:28: #2 alternative fragment length(s) may be 332 bps INFO @ Tue, 30 Jun 2020 01:45:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.05_model.r INFO @ Tue, 30 Jun 2020 01:45:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:45:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:45:29: 2000000 INFO @ Tue, 30 Jun 2020 01:45:30: 6000000 INFO @ Tue, 30 Jun 2020 01:45:37: 3000000 INFO @ Tue, 30 Jun 2020 01:45:37: 7000000 INFO @ Tue, 30 Jun 2020 01:45:45: 4000000 INFO @ Tue, 30 Jun 2020 01:45:45: 8000000 INFO @ Tue, 30 Jun 2020 01:45:52: 5000000 INFO @ Tue, 30 Jun 2020 01:45:53: 9000000 INFO @ Tue, 30 Jun 2020 01:45:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:00: 6000000 INFO @ Tue, 30 Jun 2020 01:46:01: 10000000 INFO @ Tue, 30 Jun 2020 01:46:02: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 01:46:02: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 01:46:02: #1 total tags in treatment: 10129068 INFO @ Tue, 30 Jun 2020 01:46:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:02: #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 01:46:03: #1 tags after filtering in treatment: 10129035 INFO @ Tue, 30 Jun 2020 01:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:03: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:04: #2 number of paired peaks: 182 WARNING @ Tue, 30 Jun 2020 01:46:04: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:04: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:04: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:04: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:04: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:04: #2 predicted fragment length is 332 bps INFO @ Tue, 30 Jun 2020 01:46:04: #2 alternative fragment length(s) may be 332 bps INFO @ Tue, 30 Jun 2020 01:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.10_model.r INFO @ Tue, 30 Jun 2020 01:46:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:07: 7000000 INFO @ Tue, 30 Jun 2020 01:46:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.05_summits.bed INFO @ Tue, 30 Jun 2020 01:46:08: Done! pass1 - making usageList (298 chroms): 3 millis pass2 - checking and writing primary data (10225 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:46:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:46:22: 9000000 INFO @ Tue, 30 Jun 2020 01:46:29: 10000000 INFO @ Tue, 30 Jun 2020 01:46:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:30: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 01:46:30: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 01:46:30: #1 total tags in treatment: 10129068 INFO @ Tue, 30 Jun 2020 01:46:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:30: #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 01:46:31: #1 tags after filtering in treatment: 10129035 INFO @ Tue, 30 Jun 2020 01:46:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:31: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:32: #2 number of paired peaks: 182 WARNING @ Tue, 30 Jun 2020 01:46:32: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:32: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:32: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:32: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:32: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:32: #2 predicted fragment length is 332 bps INFO @ Tue, 30 Jun 2020 01:46:32: #2 alternative fragment length(s) may be 332 bps INFO @ Tue, 30 Jun 2020 01:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.20_model.r INFO @ Tue, 30 Jun 2020 01:46:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.10_summits.bed INFO @ Tue, 30 Jun 2020 01:46:43: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (3806 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:46:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042244/SRX042244.20_summits.bed INFO @ Tue, 30 Jun 2020 01:47:10: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (678 records, 4 fields): 7 millis CompletedMACS2peakCalling