Job ID = 14170373 SRX = SRX9720908 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31458708 spots for SRR13291898/SRR13291898.sra Written 31458708 spots for SRR13291898/SRR13291898.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170788 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:42 31458708 reads; of these: 31458708 (100.00%) were unpaired; of these: 1479239 (4.70%) aligned 0 times 21909555 (69.65%) aligned exactly 1 time 8069914 (25.65%) aligned >1 times 95.30% overall alignment rate Time searching: 00:11:42 Overall time: 00:11:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5755004 / 29979469 = 0.1920 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.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 @ Sat, 11 Dec 2021 06:44:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:44:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:44:49: 1000000 INFO @ Sat, 11 Dec 2021 06:44:55: 2000000 INFO @ Sat, 11 Dec 2021 06:45:01: 3000000 INFO @ Sat, 11 Dec 2021 06:45:06: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:45:12: 5000000 INFO @ Sat, 11 Dec 2021 06:45:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.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 @ Sat, 11 Dec 2021 06:45:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:45:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:45:19: 6000000 INFO @ Sat, 11 Dec 2021 06:45:19: 1000000 INFO @ Sat, 11 Dec 2021 06:45:25: 7000000 INFO @ Sat, 11 Dec 2021 06:45:25: 2000000 INFO @ Sat, 11 Dec 2021 06:45:31: 8000000 INFO @ Sat, 11 Dec 2021 06:45:31: 3000000 INFO @ Sat, 11 Dec 2021 06:45:38: 9000000 INFO @ Sat, 11 Dec 2021 06:45:38: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:45:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.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 @ Sat, 11 Dec 2021 06:45:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:45:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:45:44: 10000000 INFO @ Sat, 11 Dec 2021 06:45:44: 5000000 INFO @ Sat, 11 Dec 2021 06:45:50: 6000000 INFO @ Sat, 11 Dec 2021 06:45:51: 11000000 INFO @ Sat, 11 Dec 2021 06:45:51: 1000000 INFO @ Sat, 11 Dec 2021 06:45:57: 7000000 INFO @ Sat, 11 Dec 2021 06:45:57: 12000000 INFO @ Sat, 11 Dec 2021 06:45:59: 2000000 INFO @ Sat, 11 Dec 2021 06:46:04: 8000000 INFO @ Sat, 11 Dec 2021 06:46:04: 13000000 INFO @ Sat, 11 Dec 2021 06:46:07: 3000000 INFO @ Sat, 11 Dec 2021 06:46:10: 9000000 INFO @ Sat, 11 Dec 2021 06:46:11: 14000000 INFO @ Sat, 11 Dec 2021 06:46:14: 4000000 INFO @ Sat, 11 Dec 2021 06:46:17: 10000000 INFO @ Sat, 11 Dec 2021 06:46:17: 15000000 INFO @ Sat, 11 Dec 2021 06:46:22: 5000000 INFO @ Sat, 11 Dec 2021 06:46:23: 11000000 INFO @ Sat, 11 Dec 2021 06:46:24: 16000000 INFO @ Sat, 11 Dec 2021 06:46:30: 12000000 INFO @ Sat, 11 Dec 2021 06:46:30: 6000000 INFO @ Sat, 11 Dec 2021 06:46:31: 17000000 INFO @ Sat, 11 Dec 2021 06:46:36: 13000000 INFO @ Sat, 11 Dec 2021 06:46:38: 18000000 INFO @ Sat, 11 Dec 2021 06:46:38: 7000000 INFO @ Sat, 11 Dec 2021 06:46:43: 14000000 INFO @ Sat, 11 Dec 2021 06:46:44: 19000000 INFO @ Sat, 11 Dec 2021 06:46:46: 8000000 INFO @ Sat, 11 Dec 2021 06:46:49: 15000000 INFO @ Sat, 11 Dec 2021 06:46:51: 20000000 INFO @ Sat, 11 Dec 2021 06:46:54: 9000000 INFO @ Sat, 11 Dec 2021 06:46:56: 16000000 INFO @ Sat, 11 Dec 2021 06:46:58: 21000000 INFO @ Sat, 11 Dec 2021 06:47:02: 10000000 INFO @ Sat, 11 Dec 2021 06:47:02: 17000000 INFO @ Sat, 11 Dec 2021 06:47:04: 22000000 INFO @ Sat, 11 Dec 2021 06:47:08: 18000000 INFO @ Sat, 11 Dec 2021 06:47:10: 11000000 INFO @ Sat, 11 Dec 2021 06:47:11: 23000000 INFO @ Sat, 11 Dec 2021 06:47:15: 19000000 INFO @ Sat, 11 Dec 2021 06:47:17: 12000000 INFO @ Sat, 11 Dec 2021 06:47:17: 24000000 INFO @ Sat, 11 Dec 2021 06:47:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:19: #1 total tags in treatment: 24224465 INFO @ Sat, 11 Dec 2021 06:47:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:47:19: #1 tags after filtering in treatment: 24224465 INFO @ Sat, 11 Dec 2021 06:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:19: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:21: 20000000 INFO @ Sat, 11 Dec 2021 06:47:21: #2 number of paired peaks: 266 WARNING @ Sat, 11 Dec 2021 06:47:21: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:21: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:21: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:21: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:21: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:21: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 06:47:21: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 11 Dec 2021 06:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.05_model.r INFO @ Sat, 11 Dec 2021 06:47:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:25: 13000000 INFO @ Sat, 11 Dec 2021 06:47:27: 21000000 INFO @ Sat, 11 Dec 2021 06:47:32: 14000000 INFO @ Sat, 11 Dec 2021 06:47:34: 22000000 INFO @ Sat, 11 Dec 2021 06:47:40: 15000000 INFO @ Sat, 11 Dec 2021 06:47:41: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:47:47: 24000000 INFO @ Sat, 11 Dec 2021 06:47:47: 16000000 INFO @ Sat, 11 Dec 2021 06:47:49: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:49: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:49: #1 total tags in treatment: 24224465 INFO @ Sat, 11 Dec 2021 06:47:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:47:49: #1 tags after filtering in treatment: 24224465 INFO @ Sat, 11 Dec 2021 06:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:49: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:51: #2 number of paired peaks: 266 WARNING @ Sat, 11 Dec 2021 06:47:51: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:51: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:51: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:51: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:51: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:51: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 06:47:51: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 11 Dec 2021 06:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.10_model.r INFO @ Sat, 11 Dec 2021 06:47:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:55: 17000000 INFO @ Sat, 11 Dec 2021 06:48:03: 18000000 INFO @ Sat, 11 Dec 2021 06:48:10: 19000000 INFO @ Sat, 11 Dec 2021 06:48:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:18: 20000000 INFO @ Sat, 11 Dec 2021 06:48:25: 21000000 INFO @ Sat, 11 Dec 2021 06:48:33: 22000000 INFO @ Sat, 11 Dec 2021 06:48:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.05_summits.bed INFO @ Sat, 11 Dec 2021 06:48:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6110 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:40: 23000000 INFO @ Sat, 11 Dec 2021 06:48:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:47: 24000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:48:49: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:48:49: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:48:49: #1 total tags in treatment: 24224465 INFO @ Sat, 11 Dec 2021 06:48:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:48:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:48:49: #1 tags after filtering in treatment: 24224465 INFO @ Sat, 11 Dec 2021 06:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:48:49: #1 finished! INFO @ Sat, 11 Dec 2021 06:48:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:48:51: #2 number of paired peaks: 266 WARNING @ Sat, 11 Dec 2021 06:48:51: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sat, 11 Dec 2021 06:48:51: start model_add_line... INFO @ Sat, 11 Dec 2021 06:48:51: start X-correlation... INFO @ Sat, 11 Dec 2021 06:48:51: end of X-cor INFO @ Sat, 11 Dec 2021 06:48:51: #2 finished! INFO @ Sat, 11 Dec 2021 06:48:51: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 06:48:51: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 11 Dec 2021 06:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.20_model.r INFO @ Sat, 11 Dec 2021 06:48:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.10_summits.bed INFO @ Sat, 11 Dec 2021 06:49:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4421 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:49:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720908/SRX9720908.20_summits.bed INFO @ Sat, 11 Dec 2021 06:50:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2858 records, 4 fields): 11 millis CompletedMACS2peakCalling