Job ID = 14167365 SRX = SRX8688935 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25026530 spots for SRR12174287/SRR12174287.sra Written 25026530 spots for SRR12174287/SRR12174287.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168014 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:57 25026530 reads; of these: 25026530 (100.00%) were unpaired; of these: 812717 (3.25%) aligned 0 times 16950436 (67.73%) aligned exactly 1 time 7263377 (29.02%) aligned >1 times 96.75% overall alignment rate Time searching: 00:09:58 Overall time: 00:09:58 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] 2888457 / 24213813 = 0.1193 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 12:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.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 12:19:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:19:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:19:43: 1000000 INFO @ Fri, 10 Dec 2021 12:19:48: 2000000 INFO @ Fri, 10 Dec 2021 12:19:53: 3000000 INFO @ Fri, 10 Dec 2021 12:19:58: 4000000 INFO @ Fri, 10 Dec 2021 12:20:03: 5000000 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 12:20:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.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 12:20:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:20:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:20:08: 6000000 INFO @ Fri, 10 Dec 2021 12:20:13: 1000000 INFO @ Fri, 10 Dec 2021 12:20:14: 7000000 INFO @ Fri, 10 Dec 2021 12:20:19: 2000000 INFO @ Fri, 10 Dec 2021 12:20:19: 8000000 INFO @ Fri, 10 Dec 2021 12:20:24: 3000000 INFO @ Fri, 10 Dec 2021 12:20:24: 9000000 INFO @ Fri, 10 Dec 2021 12:20:29: 4000000 INFO @ Fri, 10 Dec 2021 12:20:30: 10000000 INFO @ Fri, 10 Dec 2021 12:20:35: 5000000 INFO @ Fri, 10 Dec 2021 12:20:35: 11000000 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 12:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.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 12:20:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:20:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:20:40: 6000000 INFO @ Fri, 10 Dec 2021 12:20:40: 12000000 INFO @ Fri, 10 Dec 2021 12:20:45: 1000000 INFO @ Fri, 10 Dec 2021 12:20:46: 7000000 INFO @ Fri, 10 Dec 2021 12:20:46: 13000000 INFO @ Fri, 10 Dec 2021 12:20:51: 8000000 INFO @ Fri, 10 Dec 2021 12:20:52: 2000000 INFO @ Fri, 10 Dec 2021 12:20:52: 14000000 INFO @ Fri, 10 Dec 2021 12:20:57: 9000000 INFO @ Fri, 10 Dec 2021 12:20:57: 15000000 INFO @ Fri, 10 Dec 2021 12:20:58: 3000000 INFO @ Fri, 10 Dec 2021 12:21:03: 10000000 INFO @ Fri, 10 Dec 2021 12:21:03: 16000000 INFO @ Fri, 10 Dec 2021 12:21:04: 4000000 INFO @ Fri, 10 Dec 2021 12:21:08: 11000000 INFO @ Fri, 10 Dec 2021 12:21:08: 17000000 INFO @ Fri, 10 Dec 2021 12:21:11: 5000000 INFO @ Fri, 10 Dec 2021 12:21:14: 18000000 INFO @ Fri, 10 Dec 2021 12:21:14: 12000000 INFO @ Fri, 10 Dec 2021 12:21:17: 6000000 INFO @ Fri, 10 Dec 2021 12:21:19: 19000000 INFO @ Fri, 10 Dec 2021 12:21:19: 13000000 INFO @ Fri, 10 Dec 2021 12:21:24: 7000000 INFO @ Fri, 10 Dec 2021 12:21:25: 20000000 INFO @ Fri, 10 Dec 2021 12:21:25: 14000000 INFO @ Fri, 10 Dec 2021 12:21:30: 8000000 INFO @ Fri, 10 Dec 2021 12:21:31: 21000000 INFO @ Fri, 10 Dec 2021 12:21:31: 15000000 INFO @ Fri, 10 Dec 2021 12:21:33: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:21:33: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:21:33: #1 total tags in treatment: 21325356 INFO @ Fri, 10 Dec 2021 12:21:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:21:33: #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 12:21:33: #1 tags after filtering in treatment: 21325356 INFO @ Fri, 10 Dec 2021 12:21:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:21:33: #1 finished! INFO @ Fri, 10 Dec 2021 12:21:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:21:34: #2 number of paired peaks: 113 WARNING @ Fri, 10 Dec 2021 12:21:34: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Fri, 10 Dec 2021 12:21:34: start model_add_line... INFO @ Fri, 10 Dec 2021 12:21:34: start X-correlation... INFO @ Fri, 10 Dec 2021 12:21:34: end of X-cor INFO @ Fri, 10 Dec 2021 12:21:34: #2 finished! INFO @ Fri, 10 Dec 2021 12:21:34: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:21:34: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 10 Dec 2021 12:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.05_model.r WARNING @ Fri, 10 Dec 2021 12:21:34: #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 12:21:34: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 10 Dec 2021 12:21:34: #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 12:21:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:21:36: 16000000 INFO @ Fri, 10 Dec 2021 12:21:37: 9000000 INFO @ Fri, 10 Dec 2021 12:21:42: 17000000 INFO @ Fri, 10 Dec 2021 12:21:43: 10000000 INFO @ Fri, 10 Dec 2021 12:21:47: 18000000 INFO @ Fri, 10 Dec 2021 12:21:50: 11000000 INFO @ Fri, 10 Dec 2021 12:21:53: 19000000 INFO @ Fri, 10 Dec 2021 12:21:56: 12000000 INFO @ Fri, 10 Dec 2021 12:21:58: 20000000 INFO @ Fri, 10 Dec 2021 12:22:03: 13000000 INFO @ Fri, 10 Dec 2021 12:22:04: 21000000 INFO @ Fri, 10 Dec 2021 12:22:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:22:06: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:22:06: #1 total tags in treatment: 21325356 INFO @ Fri, 10 Dec 2021 12:22:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:22:06: #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 12:22:06: #1 tags after filtering in treatment: 21325356 INFO @ Fri, 10 Dec 2021 12:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:22:06: #1 finished! INFO @ Fri, 10 Dec 2021 12:22:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:22:07: #2 number of paired peaks: 113 WARNING @ Fri, 10 Dec 2021 12:22:07: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Fri, 10 Dec 2021 12:22:07: start model_add_line... INFO @ Fri, 10 Dec 2021 12:22:07: start X-correlation... INFO @ Fri, 10 Dec 2021 12:22:07: end of X-cor INFO @ Fri, 10 Dec 2021 12:22:07: #2 finished! INFO @ Fri, 10 Dec 2021 12:22:07: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:22:07: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 10 Dec 2021 12:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.10_model.r WARNING @ Fri, 10 Dec 2021 12:22:07: #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 12:22:07: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 10 Dec 2021 12:22:07: #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 12:22:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:22:09: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:22:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:22:15: 15000000 INFO @ Fri, 10 Dec 2021 12:22:21: 16000000 INFO @ Fri, 10 Dec 2021 12:22:26: 17000000 INFO @ Fri, 10 Dec 2021 12:22:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:22:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.05_summits.bed INFO @ Fri, 10 Dec 2021 12:22:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1884 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:22:32: 18000000 INFO @ Fri, 10 Dec 2021 12:22:38: 19000000 INFO @ Fri, 10 Dec 2021 12:22:44: 20000000 INFO @ Fri, 10 Dec 2021 12:22:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:22:50: 21000000 INFO @ Fri, 10 Dec 2021 12:22:52: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:22:52: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:22:52: #1 total tags in treatment: 21325356 INFO @ Fri, 10 Dec 2021 12:22:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:22:52: #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 12:22:53: #1 tags after filtering in treatment: 21325356 INFO @ Fri, 10 Dec 2021 12:22:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:22:53: #1 finished! INFO @ Fri, 10 Dec 2021 12:22:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:22:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:22:54: #2 number of paired peaks: 113 WARNING @ Fri, 10 Dec 2021 12:22:54: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Fri, 10 Dec 2021 12:22:54: start model_add_line... INFO @ Fri, 10 Dec 2021 12:22:54: start X-correlation... INFO @ Fri, 10 Dec 2021 12:22:54: end of X-cor INFO @ Fri, 10 Dec 2021 12:22:54: #2 finished! INFO @ Fri, 10 Dec 2021 12:22:54: #2 predicted fragment length is 41 bps INFO @ Fri, 10 Dec 2021 12:22:54: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 10 Dec 2021 12:22:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.20_model.r WARNING @ Fri, 10 Dec 2021 12:22:54: #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 12:22:54: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 10 Dec 2021 12:22:54: #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 12:22:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:22:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:23:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:23:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:23:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.10_summits.bed INFO @ Fri, 10 Dec 2021 12:23:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1342 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:23:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:23:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:23:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:23:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688935/SRX8688935.20_summits.bed INFO @ Fri, 10 Dec 2021 12:23:48: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (982 records, 4 fields): 2 millis CompletedMACS2peakCalling