Job ID = 14167367 SRX = SRX8688936 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21602640 spots for SRR12174288/SRR12174288.sra Written 21602640 spots for SRR12174288/SRR12174288.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168015 ("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: 00:09:40 21602640 reads; of these: 21602640 (100.00%) were unpaired; of these: 636551 (2.95%) aligned 0 times 14106030 (65.30%) aligned exactly 1 time 6860059 (31.76%) aligned >1 times 97.05% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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] 2664911 / 20966089 = 0.1271 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 @ Fri, 10 Dec 2021 12:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.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 @ Fri, 10 Dec 2021 12:18:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:18:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:18:14: 1000000 INFO @ Fri, 10 Dec 2021 12:18:21: 2000000 INFO @ Fri, 10 Dec 2021 12:18:29: 3000000 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 @ Fri, 10 Dec 2021 12:18:36: 4000000 INFO @ Fri, 10 Dec 2021 12:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.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 @ Fri, 10 Dec 2021 12:18:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:18:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:18:44: 1000000 INFO @ Fri, 10 Dec 2021 12:18:44: 5000000 INFO @ Fri, 10 Dec 2021 12:18:51: 2000000 INFO @ Fri, 10 Dec 2021 12:18:51: 6000000 INFO @ Fri, 10 Dec 2021 12:18:58: 3000000 INFO @ Fri, 10 Dec 2021 12:18:59: 7000000 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 @ Fri, 10 Dec 2021 12:19:05: 4000000 INFO @ Fri, 10 Dec 2021 12:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.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 @ Fri, 10 Dec 2021 12:19:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:19:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:19:07: 8000000 INFO @ Fri, 10 Dec 2021 12:19:12: 5000000 INFO @ Fri, 10 Dec 2021 12:19:14: 1000000 INFO @ Fri, 10 Dec 2021 12:19:14: 9000000 INFO @ Fri, 10 Dec 2021 12:19:19: 6000000 INFO @ Fri, 10 Dec 2021 12:19:21: 2000000 INFO @ Fri, 10 Dec 2021 12:19:22: 10000000 INFO @ Fri, 10 Dec 2021 12:19:26: 7000000 INFO @ Fri, 10 Dec 2021 12:19:28: 3000000 INFO @ Fri, 10 Dec 2021 12:19:30: 11000000 INFO @ Fri, 10 Dec 2021 12:19:34: 8000000 INFO @ Fri, 10 Dec 2021 12:19:36: 4000000 INFO @ Fri, 10 Dec 2021 12:19:37: 12000000 INFO @ Fri, 10 Dec 2021 12:19:41: 9000000 INFO @ Fri, 10 Dec 2021 12:19:44: 5000000 INFO @ Fri, 10 Dec 2021 12:19:45: 13000000 INFO @ Fri, 10 Dec 2021 12:19:49: 10000000 INFO @ Fri, 10 Dec 2021 12:19:52: 6000000 INFO @ Fri, 10 Dec 2021 12:19:53: 14000000 INFO @ Fri, 10 Dec 2021 12:19:56: 11000000 INFO @ Fri, 10 Dec 2021 12:19:59: 7000000 INFO @ Fri, 10 Dec 2021 12:20:01: 15000000 INFO @ Fri, 10 Dec 2021 12:20:03: 12000000 INFO @ Fri, 10 Dec 2021 12:20:07: 8000000 INFO @ Fri, 10 Dec 2021 12:20:08: 16000000 INFO @ Fri, 10 Dec 2021 12:20:10: 13000000 INFO @ Fri, 10 Dec 2021 12:20:14: 9000000 INFO @ Fri, 10 Dec 2021 12:20:16: 17000000 INFO @ Fri, 10 Dec 2021 12:20:17: 14000000 INFO @ Fri, 10 Dec 2021 12:20:21: 10000000 INFO @ Fri, 10 Dec 2021 12:20:24: 18000000 INFO @ Fri, 10 Dec 2021 12:20:24: 15000000 INFO @ Fri, 10 Dec 2021 12:20:26: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:20:26: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:20:26: #1 total tags in treatment: 18301178 INFO @ Fri, 10 Dec 2021 12:20:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:20:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:20:26: #1 tags after filtering in treatment: 18301178 INFO @ Fri, 10 Dec 2021 12:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:20:26: #1 finished! INFO @ Fri, 10 Dec 2021 12:20:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:20:28: #2 number of paired peaks: 263 WARNING @ Fri, 10 Dec 2021 12:20:28: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Fri, 10 Dec 2021 12:20:28: start model_add_line... INFO @ Fri, 10 Dec 2021 12:20:28: start X-correlation... INFO @ Fri, 10 Dec 2021 12:20:28: end of X-cor INFO @ Fri, 10 Dec 2021 12:20:28: #2 finished! INFO @ Fri, 10 Dec 2021 12:20:28: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:20:28: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 10 Dec 2021 12:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.05_model.r WARNING @ Fri, 10 Dec 2021 12:20:28: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:20:28: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 10 Dec 2021 12:20:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:20:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:20:28: 11000000 INFO @ Fri, 10 Dec 2021 12:20:31: 16000000 INFO @ Fri, 10 Dec 2021 12:20:35: 12000000 INFO @ Fri, 10 Dec 2021 12:20:38: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:20:43: 13000000 INFO @ Fri, 10 Dec 2021 12:20:45: 18000000 INFO @ Fri, 10 Dec 2021 12:20:47: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:20:47: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:20:47: #1 total tags in treatment: 18301178 INFO @ Fri, 10 Dec 2021 12:20:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:20:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:20:47: #1 tags after filtering in treatment: 18301178 INFO @ Fri, 10 Dec 2021 12:20:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:20:47: #1 finished! INFO @ Fri, 10 Dec 2021 12:20:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:20:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:20:48: #2 number of paired peaks: 263 WARNING @ Fri, 10 Dec 2021 12:20:48: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Fri, 10 Dec 2021 12:20:48: start model_add_line... INFO @ Fri, 10 Dec 2021 12:20:49: start X-correlation... INFO @ Fri, 10 Dec 2021 12:20:49: end of X-cor INFO @ Fri, 10 Dec 2021 12:20:49: #2 finished! INFO @ Fri, 10 Dec 2021 12:20:49: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:20:49: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 10 Dec 2021 12:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.10_model.r WARNING @ Fri, 10 Dec 2021 12:20:49: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:20:49: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 10 Dec 2021 12:20:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:20:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:20:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:20:49: 14000000 INFO @ Fri, 10 Dec 2021 12:20:56: 15000000 INFO @ Fri, 10 Dec 2021 12:21:03: 16000000 INFO @ Fri, 10 Dec 2021 12:21:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:21:09: 17000000 INFO @ Fri, 10 Dec 2021 12:21:16: 18000000 INFO @ Fri, 10 Dec 2021 12:21:18: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:21:18: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:21:18: #1 total tags in treatment: 18301178 INFO @ Fri, 10 Dec 2021 12:21:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:21:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:21:18: #1 tags after filtering in treatment: 18301178 INFO @ Fri, 10 Dec 2021 12:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:21:18: #1 finished! INFO @ Fri, 10 Dec 2021 12:21:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:21:19: #2 number of paired peaks: 263 WARNING @ Fri, 10 Dec 2021 12:21:19: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Fri, 10 Dec 2021 12:21:19: start model_add_line... INFO @ Fri, 10 Dec 2021 12:21:19: start X-correlation... INFO @ Fri, 10 Dec 2021 12:21:19: end of X-cor INFO @ Fri, 10 Dec 2021 12:21:19: #2 finished! INFO @ Fri, 10 Dec 2021 12:21:19: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:21:19: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 10 Dec 2021 12:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.20_model.r WARNING @ Fri, 10 Dec 2021 12:21:19: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:21:19: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 10 Dec 2021 12:21:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:21:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:21:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:21:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:21:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:21:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.05_summits.bed INFO @ Fri, 10 Dec 2021 12:21:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2177 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:21:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:21:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:21:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:21:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.10_summits.bed INFO @ Fri, 10 Dec 2021 12:21:45: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1541 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:21:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:22:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:22:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:22:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688936/SRX8688936.20_summits.bed INFO @ Fri, 10 Dec 2021 12:22:18: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1187 records, 4 fields): 4 millis CompletedMACS2peakCalling