Job ID = 14170389 SRX = SRX8689010 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22498751 spots for SRR12174299/SRR12174299.sra Written 22498751 spots for SRR12174299/SRR12174299.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170805 ("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: 00:08:16 22498751 reads; of these: 22498751 (100.00%) were unpaired; of these: 573928 (2.55%) aligned 0 times 14908686 (66.26%) aligned exactly 1 time 7016137 (31.18%) aligned >1 times 97.45% overall alignment rate Time searching: 00:08:17 Overall time: 00:08:17 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] 2438368 / 21924823 = 0.1112 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 06:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.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 06:50:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:50:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:50:16: 1000000 INFO @ Sat, 11 Dec 2021 06:50:22: 2000000 INFO @ Sat, 11 Dec 2021 06:50:28: 3000000 INFO @ Sat, 11 Dec 2021 06:50:34: 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 06:50:40: 5000000 INFO @ Sat, 11 Dec 2021 06:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.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 06:50:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:50:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:50:46: 1000000 INFO @ Sat, 11 Dec 2021 06:50:46: 6000000 INFO @ Sat, 11 Dec 2021 06:50:51: 2000000 INFO @ Sat, 11 Dec 2021 06:50:52: 7000000 INFO @ Sat, 11 Dec 2021 06:50:56: 3000000 INFO @ Sat, 11 Dec 2021 06:50:58: 8000000 INFO @ Sat, 11 Dec 2021 06:51:02: 4000000 INFO @ Sat, 11 Dec 2021 06:51:04: 9000000 INFO @ Sat, 11 Dec 2021 06:51:07: 5000000 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 06:51:10: 10000000 INFO @ Sat, 11 Dec 2021 06:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.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 06:51:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:51:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:51:12: 6000000 INFO @ Sat, 11 Dec 2021 06:51:16: 11000000 INFO @ Sat, 11 Dec 2021 06:51:16: 1000000 INFO @ Sat, 11 Dec 2021 06:51:17: 7000000 INFO @ Sat, 11 Dec 2021 06:51:21: 2000000 INFO @ Sat, 11 Dec 2021 06:51:22: 12000000 INFO @ Sat, 11 Dec 2021 06:51:23: 8000000 INFO @ Sat, 11 Dec 2021 06:51:26: 3000000 INFO @ Sat, 11 Dec 2021 06:51:27: 13000000 INFO @ Sat, 11 Dec 2021 06:51:28: 9000000 INFO @ Sat, 11 Dec 2021 06:51:32: 4000000 INFO @ Sat, 11 Dec 2021 06:51:33: 10000000 INFO @ Sat, 11 Dec 2021 06:51:33: 14000000 INFO @ Sat, 11 Dec 2021 06:51:37: 5000000 INFO @ Sat, 11 Dec 2021 06:51:39: 11000000 INFO @ Sat, 11 Dec 2021 06:51:40: 15000000 INFO @ Sat, 11 Dec 2021 06:51:42: 6000000 INFO @ Sat, 11 Dec 2021 06:51:44: 12000000 INFO @ Sat, 11 Dec 2021 06:51:46: 16000000 INFO @ Sat, 11 Dec 2021 06:51:48: 7000000 INFO @ Sat, 11 Dec 2021 06:51:49: 13000000 INFO @ Sat, 11 Dec 2021 06:51:52: 17000000 INFO @ Sat, 11 Dec 2021 06:51:53: 8000000 INFO @ Sat, 11 Dec 2021 06:51:54: 14000000 INFO @ Sat, 11 Dec 2021 06:51:58: 18000000 INFO @ Sat, 11 Dec 2021 06:51:58: 9000000 INFO @ Sat, 11 Dec 2021 06:52:00: 15000000 INFO @ Sat, 11 Dec 2021 06:52:04: 10000000 INFO @ Sat, 11 Dec 2021 06:52:04: 19000000 INFO @ Sat, 11 Dec 2021 06:52:05: 16000000 INFO @ Sat, 11 Dec 2021 06:52:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:52:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:52:07: #1 total tags in treatment: 19486455 INFO @ Sat, 11 Dec 2021 06:52:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:07: #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 06:52:07: #1 tags after filtering in treatment: 19486455 INFO @ Sat, 11 Dec 2021 06:52:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:07: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:08: #2 number of paired peaks: 148 WARNING @ Sat, 11 Dec 2021 06:52:08: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:08: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:08: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:08: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:08: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:08: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 06:52:08: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 11 Dec 2021 06:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.05_model.r WARNING @ Sat, 11 Dec 2021 06:52:08: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:52:08: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 11 Dec 2021 06:52:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:52:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:52:09: 11000000 INFO @ Sat, 11 Dec 2021 06:52:10: 17000000 INFO @ Sat, 11 Dec 2021 06:52:14: 12000000 INFO @ Sat, 11 Dec 2021 06:52:16: 18000000 INFO @ Sat, 11 Dec 2021 06:52:19: 13000000 INFO @ Sat, 11 Dec 2021 06:52:21: 19000000 INFO @ Sat, 11 Dec 2021 06:52:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:52:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:52:23: #1 total tags in treatment: 19486455 INFO @ Sat, 11 Dec 2021 06:52:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:23: #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 06:52:24: #1 tags after filtering in treatment: 19486455 INFO @ Sat, 11 Dec 2021 06:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:24: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:24: 14000000 INFO @ Sat, 11 Dec 2021 06:52:25: #2 number of paired peaks: 148 WARNING @ Sat, 11 Dec 2021 06:52:25: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:25: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:25: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:25: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:25: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:25: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 06:52:25: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 11 Dec 2021 06:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.10_model.r WARNING @ Sat, 11 Dec 2021 06:52:25: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:52:25: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 11 Dec 2021 06:52:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:52:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:52:29: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:52:34: 16000000 INFO @ Sat, 11 Dec 2021 06:52:39: 17000000 INFO @ Sat, 11 Dec 2021 06:52:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:52:44: 18000000 INFO @ Sat, 11 Dec 2021 06:52:49: 19000000 INFO @ Sat, 11 Dec 2021 06:52:52: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:52:52: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:52:52: #1 total tags in treatment: 19486455 INFO @ Sat, 11 Dec 2021 06:52:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:52: #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 06:52:52: #1 tags after filtering in treatment: 19486455 INFO @ Sat, 11 Dec 2021 06:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:52: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:53: #2 number of paired peaks: 148 WARNING @ Sat, 11 Dec 2021 06:52:53: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:53: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:53: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:53: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:53: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:53: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 06:52:53: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 11 Dec 2021 06:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.20_model.r WARNING @ Sat, 11 Dec 2021 06:52:53: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:52:53: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 11 Dec 2021 06:52:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:52:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:53:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.05_summits.bed INFO @ Sat, 11 Dec 2021 06:53:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2436 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.10_summits.bed INFO @ Sat, 11 Dec 2021 06:53:17: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1490 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:53:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689010/SRX8689010.20_summits.bed INFO @ Sat, 11 Dec 2021 06:53:45: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1076 records, 4 fields): 3 millis CompletedMACS2peakCalling