Job ID = 6529505 SRX = SRX287859 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: 00:05:45 19509379 reads; of these: 19509379 (100.00%) were unpaired; of these: 1161670 (5.95%) aligned 0 times 13965499 (71.58%) aligned exactly 1 time 4382210 (22.46%) aligned >1 times 94.05% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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] 2176692 / 18347709 = 0.1186 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 02:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.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 02:16:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:20: 1000000 INFO @ Tue, 30 Jun 2020 02:16:26: 2000000 INFO @ Tue, 30 Jun 2020 02:16:32: 3000000 INFO @ Tue, 30 Jun 2020 02:16:38: 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 02:16:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.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 02:16:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:44: 5000000 INFO @ Tue, 30 Jun 2020 02:16:50: 1000000 INFO @ Tue, 30 Jun 2020 02:16:51: 6000000 INFO @ Tue, 30 Jun 2020 02:16:57: 2000000 INFO @ Tue, 30 Jun 2020 02:16:57: 7000000 INFO @ Tue, 30 Jun 2020 02:17:03: 3000000 INFO @ Tue, 30 Jun 2020 02:17:04: 8000000 INFO @ Tue, 30 Jun 2020 02:17:09: 4000000 INFO @ Tue, 30 Jun 2020 02:17:10: 9000000 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 02:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.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 02:17:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:16: 5000000 INFO @ Tue, 30 Jun 2020 02:17:16: 10000000 INFO @ Tue, 30 Jun 2020 02:17:20: 1000000 INFO @ Tue, 30 Jun 2020 02:17:23: 11000000 INFO @ Tue, 30 Jun 2020 02:17:23: 6000000 INFO @ Tue, 30 Jun 2020 02:17:27: 2000000 INFO @ Tue, 30 Jun 2020 02:17:29: 12000000 INFO @ Tue, 30 Jun 2020 02:17:29: 7000000 INFO @ Tue, 30 Jun 2020 02:17:33: 3000000 INFO @ Tue, 30 Jun 2020 02:17:36: 13000000 INFO @ Tue, 30 Jun 2020 02:17:36: 8000000 INFO @ Tue, 30 Jun 2020 02:17:40: 4000000 INFO @ Tue, 30 Jun 2020 02:17:42: 14000000 INFO @ Tue, 30 Jun 2020 02:17:43: 9000000 INFO @ Tue, 30 Jun 2020 02:17:47: 5000000 INFO @ Tue, 30 Jun 2020 02:17:49: 15000000 INFO @ Tue, 30 Jun 2020 02:17:49: 10000000 INFO @ Tue, 30 Jun 2020 02:17:53: 6000000 INFO @ Tue, 30 Jun 2020 02:17:55: 11000000 INFO @ Tue, 30 Jun 2020 02:17:56: 16000000 INFO @ Tue, 30 Jun 2020 02:17:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:17:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:17:57: #1 total tags in treatment: 16171017 INFO @ Tue, 30 Jun 2020 02:17:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:57: #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 02:17:57: #1 tags after filtering in treatment: 16171003 INFO @ Tue, 30 Jun 2020 02:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:59: #2 number of paired peaks: 461 WARNING @ Tue, 30 Jun 2020 02:17:59: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:59: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:59: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:59: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:59: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:59: #2 predicted fragment length is 124 bps INFO @ Tue, 30 Jun 2020 02:17:59: #2 alternative fragment length(s) may be 93,124,572 bps INFO @ Tue, 30 Jun 2020 02:17:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.05_model.r INFO @ Tue, 30 Jun 2020 02:17:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:00: 7000000 INFO @ Tue, 30 Jun 2020 02:18:02: 12000000 INFO @ Tue, 30 Jun 2020 02:18:07: 8000000 INFO @ Tue, 30 Jun 2020 02:18:08: 13000000 INFO @ Tue, 30 Jun 2020 02:18:13: 9000000 INFO @ Tue, 30 Jun 2020 02:18:15: 14000000 INFO @ Tue, 30 Jun 2020 02:18:20: 10000000 INFO @ Tue, 30 Jun 2020 02:18:22: 15000000 INFO @ Tue, 30 Jun 2020 02:18:26: 11000000 INFO @ Tue, 30 Jun 2020 02:18:29: 16000000 INFO @ Tue, 30 Jun 2020 02:18:30: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:18:30: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:18:30: #1 total tags in treatment: 16171017 INFO @ Tue, 30 Jun 2020 02:18:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:30: #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 02:18:31: #1 tags after filtering in treatment: 16171003 INFO @ Tue, 30 Jun 2020 02:18:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:32: #2 number of paired peaks: 461 WARNING @ Tue, 30 Jun 2020 02:18:32: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:32: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:32: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:32: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:32: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:32: #2 predicted fragment length is 124 bps INFO @ Tue, 30 Jun 2020 02:18:32: #2 alternative fragment length(s) may be 93,124,572 bps INFO @ Tue, 30 Jun 2020 02:18:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.10_model.r INFO @ Tue, 30 Jun 2020 02:18:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:32: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:18:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:39: 13000000 INFO @ Tue, 30 Jun 2020 02:18:45: 14000000 INFO @ Tue, 30 Jun 2020 02:18:51: 15000000 INFO @ Tue, 30 Jun 2020 02:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.05_summits.bed INFO @ Tue, 30 Jun 2020 02:18:55: Done! pass1 - making usageList (602 chroms): 2 millis pass2 - checking and writing primary data (2812 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:18:58: 16000000 INFO @ Tue, 30 Jun 2020 02:18:59: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:18:59: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:18:59: #1 total tags in treatment: 16171017 INFO @ Tue, 30 Jun 2020 02:18:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:59: #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 02:19:00: #1 tags after filtering in treatment: 16171003 INFO @ Tue, 30 Jun 2020 02:19:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:00: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:01: #2 number of paired peaks: 461 WARNING @ Tue, 30 Jun 2020 02:19:01: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:01: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:01: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:01: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:01: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:01: #2 predicted fragment length is 124 bps INFO @ Tue, 30 Jun 2020 02:19:01: #2 alternative fragment length(s) may be 93,124,572 bps INFO @ Tue, 30 Jun 2020 02:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.20_model.r INFO @ Tue, 30 Jun 2020 02:19:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:19:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.10_summits.bed INFO @ Tue, 30 Jun 2020 02:19:31: Done! pass1 - making usageList (396 chroms): 1 millis pass2 - checking and writing primary data (1202 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:19:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287859/SRX287859.20_summits.bed INFO @ Tue, 30 Jun 2020 02:19:59: Done! pass1 - making usageList (271 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 11 millis CompletedMACS2peakCalling