Job ID = 6529206 SRX = SRX041395 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: 00:00:01 Multiseed full-index search: 00:03:27 19660324 reads; of these: 19660324 (100.00%) were unpaired; of these: 932682 (4.74%) aligned 0 times 15797586 (80.35%) aligned exactly 1 time 2930056 (14.90%) aligned >1 times 95.26% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 2506053 / 18727642 = 0.1338 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 01:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.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 01:57:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:08: 1000000 INFO @ Tue, 30 Jun 2020 01:57:14: 2000000 INFO @ Tue, 30 Jun 2020 01:57:19: 3000000 INFO @ Tue, 30 Jun 2020 01:57:24: 4000000 INFO @ Tue, 30 Jun 2020 01:57:30: 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 01:57:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.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 01:57:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:35: 6000000 INFO @ Tue, 30 Jun 2020 01:57:39: 1000000 INFO @ Tue, 30 Jun 2020 01:57:41: 7000000 INFO @ Tue, 30 Jun 2020 01:57:45: 2000000 INFO @ Tue, 30 Jun 2020 01:57:47: 8000000 INFO @ Tue, 30 Jun 2020 01:57:51: 3000000 INFO @ Tue, 30 Jun 2020 01:57:53: 9000000 INFO @ Tue, 30 Jun 2020 01:57:57: 4000000 INFO @ Tue, 30 Jun 2020 01:58:00: 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 01:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.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 01:58:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:03: 5000000 INFO @ Tue, 30 Jun 2020 01:58:06: 11000000 INFO @ Tue, 30 Jun 2020 01:58:09: 1000000 INFO @ Tue, 30 Jun 2020 01:58:10: 6000000 INFO @ Tue, 30 Jun 2020 01:58:12: 12000000 INFO @ Tue, 30 Jun 2020 01:58:15: 2000000 INFO @ Tue, 30 Jun 2020 01:58:16: 7000000 INFO @ Tue, 30 Jun 2020 01:58:18: 13000000 INFO @ Tue, 30 Jun 2020 01:58:22: 3000000 INFO @ Tue, 30 Jun 2020 01:58:22: 8000000 INFO @ Tue, 30 Jun 2020 01:58:25: 14000000 INFO @ Tue, 30 Jun 2020 01:58:28: 4000000 INFO @ Tue, 30 Jun 2020 01:58:28: 9000000 INFO @ Tue, 30 Jun 2020 01:58:31: 15000000 INFO @ Tue, 30 Jun 2020 01:58:34: 5000000 INFO @ Tue, 30 Jun 2020 01:58:34: 10000000 INFO @ Tue, 30 Jun 2020 01:58:37: 16000000 INFO @ Tue, 30 Jun 2020 01:58:39: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:58:39: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:58:39: #1 total tags in treatment: 16221589 INFO @ Tue, 30 Jun 2020 01:58:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:39: #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 01:58:39: #1 tags after filtering in treatment: 16221580 INFO @ Tue, 30 Jun 2020 01:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:39: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:40: 6000000 INFO @ Tue, 30 Jun 2020 01:58:40: #2 number of paired peaks: 136 WARNING @ Tue, 30 Jun 2020 01:58:40: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:40: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:40: 11000000 INFO @ Tue, 30 Jun 2020 01:58:41: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:41: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:41: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:41: #2 predicted fragment length is 150 bps INFO @ Tue, 30 Jun 2020 01:58:41: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 30 Jun 2020 01:58:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.05_model.r INFO @ Tue, 30 Jun 2020 01:58:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:47: 7000000 INFO @ Tue, 30 Jun 2020 01:58:47: 12000000 INFO @ Tue, 30 Jun 2020 01:58:53: 8000000 INFO @ Tue, 30 Jun 2020 01:58:53: 13000000 INFO @ Tue, 30 Jun 2020 01:58:59: 9000000 INFO @ Tue, 30 Jun 2020 01:58:59: 14000000 INFO @ Tue, 30 Jun 2020 01:59:05: 10000000 INFO @ Tue, 30 Jun 2020 01:59:06: 15000000 INFO @ Tue, 30 Jun 2020 01:59:11: 11000000 INFO @ Tue, 30 Jun 2020 01:59:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:12: 16000000 INFO @ Tue, 30 Jun 2020 01:59:13: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:59:13: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:59:13: #1 total tags in treatment: 16221589 INFO @ Tue, 30 Jun 2020 01:59:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:13: #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 01:59:14: #1 tags after filtering in treatment: 16221580 INFO @ Tue, 30 Jun 2020 01:59:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:14: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:15: #2 number of paired peaks: 136 WARNING @ Tue, 30 Jun 2020 01:59:15: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:15: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:15: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:15: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:15: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:15: #2 predicted fragment length is 150 bps INFO @ Tue, 30 Jun 2020 01:59:15: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 30 Jun 2020 01:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.10_model.r INFO @ Tue, 30 Jun 2020 01:59:15: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:59:17: 12000000 INFO @ Tue, 30 Jun 2020 01:59:23: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:59:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.05_summits.bed INFO @ Tue, 30 Jun 2020 01:59:27: Done! pass1 - making usageList (144 chroms): 2 millis pass2 - checking and writing primary data (7656 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:59:29: 14000000 INFO @ Tue, 30 Jun 2020 01:59:34: 15000000 INFO @ Tue, 30 Jun 2020 01:59:39: 16000000 INFO @ Tue, 30 Jun 2020 01:59:41: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:59:41: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:59:41: #1 total tags in treatment: 16221589 INFO @ Tue, 30 Jun 2020 01:59:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:41: #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 01:59:41: #1 tags after filtering in treatment: 16221580 INFO @ Tue, 30 Jun 2020 01:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:41: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:42: #2 number of paired peaks: 136 WARNING @ Tue, 30 Jun 2020 01:59:42: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:42: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:42: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:42: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:42: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:42: #2 predicted fragment length is 150 bps INFO @ Tue, 30 Jun 2020 01:59:42: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 30 Jun 2020 01:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.20_model.r INFO @ Tue, 30 Jun 2020 01:59:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:59:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:00:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:00:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.10_summits.bed INFO @ Tue, 30 Jun 2020 02:00:02: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (2795 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:00:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041395/SRX041395.20_summits.bed INFO @ Tue, 30 Jun 2020 02:00:33: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 3 millis CompletedMACS2peakCalling