Job ID = 16439631 SRX = SRX13572049 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11753476 spots for SRR17399996/SRR17399996.sra Written 11753476 spots for SRR17399996/SRR17399996.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439667 ("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: 00:03:00 11753476 reads; of these: 11753476 (100.00%) were unpaired; of these: 729746 (6.21%) aligned 0 times 9491854 (80.76%) aligned exactly 1 time 1531876 (13.03%) aligned >1 times 93.79% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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 8 files... [bam_rmdupse_core] 595275 / 11023730 = 0.0540 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 15:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.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 15:51:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:51:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:51:29: 1000000 INFO @ Tue, 02 Aug 2022 15:51:36: 2000000 INFO @ Tue, 02 Aug 2022 15:51:43: 3000000 INFO @ Tue, 02 Aug 2022 15:51:49: 4000000 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 15:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.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 15:51:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:51:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:51:56: 5000000 INFO @ Tue, 02 Aug 2022 15:52:00: 1000000 INFO @ Tue, 02 Aug 2022 15:52:03: 6000000 INFO @ Tue, 02 Aug 2022 15:52:07: 2000000 INFO @ Tue, 02 Aug 2022 15:52:09: 7000000 INFO @ Tue, 02 Aug 2022 15:52:14: 3000000 INFO @ Tue, 02 Aug 2022 15:52:16: 8000000 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 15:52:21: 4000000 INFO @ Tue, 02 Aug 2022 15:52:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.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 15:52:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:52:23: 9000000 INFO @ Tue, 02 Aug 2022 15:52:29: 5000000 INFO @ Tue, 02 Aug 2022 15:52:29: 1000000 INFO @ Tue, 02 Aug 2022 15:52:30: 10000000 INFO @ Tue, 02 Aug 2022 15:52:33: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 15:52:33: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 15:52:33: #1 total tags in treatment: 10428455 INFO @ Tue, 02 Aug 2022 15:52:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:52:33: #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 15:52:34: #1 tags after filtering in treatment: 10428455 INFO @ Tue, 02 Aug 2022 15:52:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:52:34: #1 finished! INFO @ Tue, 02 Aug 2022 15:52:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:52:34: #2 number of paired peaks: 125 WARNING @ Tue, 02 Aug 2022 15:52:34: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 02 Aug 2022 15:52:34: start model_add_line... INFO @ Tue, 02 Aug 2022 15:52:34: start X-correlation... INFO @ Tue, 02 Aug 2022 15:52:34: end of X-cor INFO @ Tue, 02 Aug 2022 15:52:34: #2 finished! INFO @ Tue, 02 Aug 2022 15:52:34: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 15:52:34: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 15:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.05_model.r INFO @ Tue, 02 Aug 2022 15:52:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:52:36: 6000000 INFO @ Tue, 02 Aug 2022 15:52:36: 2000000 INFO @ Tue, 02 Aug 2022 15:52:43: 7000000 INFO @ Tue, 02 Aug 2022 15:52:43: 3000000 INFO @ Tue, 02 Aug 2022 15:52:50: 4000000 INFO @ Tue, 02 Aug 2022 15:52:50: 8000000 INFO @ Tue, 02 Aug 2022 15:52:57: 5000000 INFO @ Tue, 02 Aug 2022 15:52:58: 9000000 INFO @ Tue, 02 Aug 2022 15:53:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:53:04: 6000000 INFO @ Tue, 02 Aug 2022 15:53:05: 10000000 INFO @ Tue, 02 Aug 2022 15:53:08: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 15:53:08: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 15:53:08: #1 total tags in treatment: 10428455 INFO @ Tue, 02 Aug 2022 15:53:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:08: #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 15:53:08: #1 tags after filtering in treatment: 10428455 INFO @ Tue, 02 Aug 2022 15:53:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:53:08: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:09: #2 number of paired peaks: 125 WARNING @ Tue, 02 Aug 2022 15:53:09: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 02 Aug 2022 15:53:09: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:09: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:09: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:09: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:09: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 15:53:09: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 15:53:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.10_model.r INFO @ Tue, 02 Aug 2022 15:53:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:53:11: 7000000 INFO @ Tue, 02 Aug 2022 15:53:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:53:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:53:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.05_summits.bed INFO @ Tue, 02 Aug 2022 15:53:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (743 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:53:17: 8000000 INFO @ Tue, 02 Aug 2022 15:53:23: 9000000 INFO @ Tue, 02 Aug 2022 15:53:30: 10000000 INFO @ Tue, 02 Aug 2022 15:53:32: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 15:53:32: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 15:53:32: #1 total tags in treatment: 10428455 INFO @ Tue, 02 Aug 2022 15:53:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:32: #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 15:53:33: #1 tags after filtering in treatment: 10428455 INFO @ Tue, 02 Aug 2022 15:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:53:33: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:33: #2 number of paired peaks: 125 WARNING @ Tue, 02 Aug 2022 15:53:33: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 02 Aug 2022 15:53:33: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:33: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:33: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:33: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:33: #2 predicted fragment length is 172 bps INFO @ Tue, 02 Aug 2022 15:53:33: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 02 Aug 2022 15:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.20_model.r INFO @ Tue, 02 Aug 2022 15:53:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:53:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.10_summits.bed INFO @ Tue, 02 Aug 2022 15:53:47: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (414 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:53:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13572049/SRX13572049.20_summits.bed INFO @ Tue, 02 Aug 2022 15:54:11: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (223 records, 4 fields): 2 millis CompletedMACS2peakCalling