Job ID = 16439710 SRX = SRX14237854 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30523636 spots for SRR18086350/SRR18086350.sra Written 30523636 spots for SRR18086350/SRR18086350.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439829 ("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: 00:11:06 30523636 reads; of these: 30523636 (100.00%) were unpaired; of these: 1588136 (5.20%) aligned 0 times 24481726 (80.21%) aligned exactly 1 time 4453774 (14.59%) aligned >1 times 94.80% overall alignment rate Time searching: 00:11:06 Overall time: 00:11:06 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 12 files... [bam_rmdupse_core] 5649377 / 28935500 = 0.1952 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.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, 02 Aug 2022 16:20:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:20:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:20:11: 1000000 INFO @ Tue, 02 Aug 2022 16:20:18: 2000000 INFO @ Tue, 02 Aug 2022 16:20:26: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.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, 02 Aug 2022 16:20:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:20:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:20:33: 4000000 INFO @ Tue, 02 Aug 2022 16:20:40: 1000000 INFO @ Tue, 02 Aug 2022 16:20:41: 5000000 INFO @ Tue, 02 Aug 2022 16:20:48: 2000000 INFO @ Tue, 02 Aug 2022 16:20:50: 6000000 INFO @ Tue, 02 Aug 2022 16:20:57: 3000000 INFO @ Tue, 02 Aug 2022 16:20:58: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.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, 02 Aug 2022 16:21:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:21:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:21:05: 4000000 INFO @ Tue, 02 Aug 2022 16:21:06: 8000000 INFO @ Tue, 02 Aug 2022 16:21:10: 1000000 INFO @ Tue, 02 Aug 2022 16:21:13: 5000000 INFO @ Tue, 02 Aug 2022 16:21:14: 9000000 INFO @ Tue, 02 Aug 2022 16:21:18: 2000000 INFO @ Tue, 02 Aug 2022 16:21:21: 6000000 INFO @ Tue, 02 Aug 2022 16:21:22: 10000000 INFO @ Tue, 02 Aug 2022 16:21:26: 3000000 INFO @ Tue, 02 Aug 2022 16:21:29: 7000000 INFO @ Tue, 02 Aug 2022 16:21:30: 11000000 INFO @ Tue, 02 Aug 2022 16:21:34: 4000000 INFO @ Tue, 02 Aug 2022 16:21:37: 8000000 INFO @ Tue, 02 Aug 2022 16:21:38: 12000000 INFO @ Tue, 02 Aug 2022 16:21:42: 5000000 INFO @ Tue, 02 Aug 2022 16:21:45: 9000000 INFO @ Tue, 02 Aug 2022 16:21:45: 13000000 INFO @ Tue, 02 Aug 2022 16:21:50: 6000000 INFO @ Tue, 02 Aug 2022 16:21:53: 10000000 INFO @ Tue, 02 Aug 2022 16:21:53: 14000000 INFO @ Tue, 02 Aug 2022 16:21:58: 7000000 INFO @ Tue, 02 Aug 2022 16:22:01: 11000000 INFO @ Tue, 02 Aug 2022 16:22:01: 15000000 INFO @ Tue, 02 Aug 2022 16:22:07: 8000000 INFO @ Tue, 02 Aug 2022 16:22:09: 12000000 INFO @ Tue, 02 Aug 2022 16:22:09: 16000000 INFO @ Tue, 02 Aug 2022 16:22:15: 9000000 INFO @ Tue, 02 Aug 2022 16:22:17: 17000000 INFO @ Tue, 02 Aug 2022 16:22:17: 13000000 INFO @ Tue, 02 Aug 2022 16:22:24: 10000000 INFO @ Tue, 02 Aug 2022 16:22:24: 18000000 INFO @ Tue, 02 Aug 2022 16:22:25: 14000000 INFO @ Tue, 02 Aug 2022 16:22:32: 19000000 INFO @ Tue, 02 Aug 2022 16:22:32: 11000000 INFO @ Tue, 02 Aug 2022 16:22:32: 15000000 INFO @ Tue, 02 Aug 2022 16:22:40: 20000000 INFO @ Tue, 02 Aug 2022 16:22:40: 16000000 INFO @ Tue, 02 Aug 2022 16:22:41: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:22:48: 21000000 INFO @ Tue, 02 Aug 2022 16:22:48: 17000000 INFO @ Tue, 02 Aug 2022 16:22:49: 13000000 INFO @ Tue, 02 Aug 2022 16:22:55: 22000000 INFO @ Tue, 02 Aug 2022 16:22:56: 18000000 INFO @ Tue, 02 Aug 2022 16:22:58: 14000000 INFO @ Tue, 02 Aug 2022 16:23:03: 23000000 INFO @ Tue, 02 Aug 2022 16:23:04: 19000000 INFO @ Tue, 02 Aug 2022 16:23:05: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:23:05: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:23:05: #1 total tags in treatment: 23286123 INFO @ Tue, 02 Aug 2022 16:23:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:23:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:23:05: #1 tags after filtering in treatment: 23286123 INFO @ Tue, 02 Aug 2022 16:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:23:05: #1 finished! INFO @ Tue, 02 Aug 2022 16:23:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:23:06: 15000000 INFO @ Tue, 02 Aug 2022 16:23:07: #2 number of paired peaks: 2440 INFO @ Tue, 02 Aug 2022 16:23:07: start model_add_line... INFO @ Tue, 02 Aug 2022 16:23:07: start X-correlation... INFO @ Tue, 02 Aug 2022 16:23:08: end of X-cor INFO @ Tue, 02 Aug 2022 16:23:08: #2 finished! INFO @ Tue, 02 Aug 2022 16:23:08: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 16:23:08: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 16:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.05_model.r INFO @ Tue, 02 Aug 2022 16:23:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:23:11: 20000000 INFO @ Tue, 02 Aug 2022 16:23:14: 16000000 INFO @ Tue, 02 Aug 2022 16:23:19: 21000000 INFO @ Tue, 02 Aug 2022 16:23:23: 17000000 INFO @ Tue, 02 Aug 2022 16:23:26: 22000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:23:31: 18000000 INFO @ Tue, 02 Aug 2022 16:23:34: 23000000 INFO @ Tue, 02 Aug 2022 16:23:36: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:23:36: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:23:36: #1 total tags in treatment: 23286123 INFO @ Tue, 02 Aug 2022 16:23:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:23:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:23:36: #1 tags after filtering in treatment: 23286123 INFO @ Tue, 02 Aug 2022 16:23:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:23:36: #1 finished! INFO @ Tue, 02 Aug 2022 16:23:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:23:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:23:38: #2 number of paired peaks: 2440 INFO @ Tue, 02 Aug 2022 16:23:38: start model_add_line... INFO @ Tue, 02 Aug 2022 16:23:38: start X-correlation... INFO @ Tue, 02 Aug 2022 16:23:38: end of X-cor INFO @ Tue, 02 Aug 2022 16:23:38: #2 finished! INFO @ Tue, 02 Aug 2022 16:23:38: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 16:23:38: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 16:23:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.10_model.r INFO @ Tue, 02 Aug 2022 16:23:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:23:39: 19000000 INFO @ Tue, 02 Aug 2022 16:23:47: 20000000 INFO @ Tue, 02 Aug 2022 16:23:54: 21000000 INFO @ Tue, 02 Aug 2022 16:24:02: 22000000 INFO @ Tue, 02 Aug 2022 16:24:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:24:09: 23000000 INFO @ Tue, 02 Aug 2022 16:24:11: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:24:11: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:24:11: #1 total tags in treatment: 23286123 INFO @ Tue, 02 Aug 2022 16:24:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:24:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:24:12: #1 tags after filtering in treatment: 23286123 INFO @ Tue, 02 Aug 2022 16:24:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:24:12: #1 finished! INFO @ Tue, 02 Aug 2022 16:24:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:24:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:24:13: #2 number of paired peaks: 2440 INFO @ Tue, 02 Aug 2022 16:24:13: start model_add_line... INFO @ Tue, 02 Aug 2022 16:24:14: start X-correlation... INFO @ Tue, 02 Aug 2022 16:24:14: end of X-cor INFO @ Tue, 02 Aug 2022 16:24:14: #2 finished! INFO @ Tue, 02 Aug 2022 16:24:14: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 16:24:14: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 16:24:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.20_model.r INFO @ Tue, 02 Aug 2022 16:24:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:24:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:24:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:24:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.05_summits.bed INFO @ Tue, 02 Aug 2022 16:24:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8041 records, 4 fields): 144 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:24:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:24:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:24:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:24:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.10_summits.bed INFO @ Tue, 02 Aug 2022 16:24:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6675 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:25:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:25:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:25:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14237854/SRX14237854.20_summits.bed INFO @ Tue, 02 Aug 2022 16:25:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5143 records, 4 fields): 49 millis CompletedMACS2peakCalling