Job ID = 14170384 SRX = SRX8689008 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23639722 spots for SRR12174297/SRR12174297.sra Written 23639722 spots for SRR12174297/SRR12174297.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170797 ("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: 00:09:41 23639722 reads; of these: 23639722 (100.00%) were unpaired; of these: 620953 (2.63%) aligned 0 times 15555513 (65.80%) aligned exactly 1 time 7463256 (31.57%) aligned >1 times 97.37% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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] 2687690 / 23018769 = 0.1168 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 06:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.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 06:49:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:49:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:49:51: 1000000 INFO @ Sat, 11 Dec 2021 06:49:57: 2000000 INFO @ Sat, 11 Dec 2021 06:50:04: 3000000 INFO @ Sat, 11 Dec 2021 06:50:10: 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 06:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.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 06:50:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:50:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:50:16: 5000000 INFO @ Sat, 11 Dec 2021 06:50:22: 1000000 INFO @ Sat, 11 Dec 2021 06:50:23: 6000000 INFO @ Sat, 11 Dec 2021 06:50:29: 2000000 INFO @ Sat, 11 Dec 2021 06:50:30: 7000000 INFO @ Sat, 11 Dec 2021 06:50:36: 3000000 INFO @ Sat, 11 Dec 2021 06:50:37: 8000000 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 06:50:43: 4000000 INFO @ Sat, 11 Dec 2021 06:50:44: 9000000 INFO @ Sat, 11 Dec 2021 06:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.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 06:50:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:50:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:50:50: 5000000 INFO @ Sat, 11 Dec 2021 06:50:51: 10000000 INFO @ Sat, 11 Dec 2021 06:50:52: 1000000 INFO @ Sat, 11 Dec 2021 06:50:57: 6000000 INFO @ Sat, 11 Dec 2021 06:50:58: 11000000 INFO @ Sat, 11 Dec 2021 06:51:00: 2000000 INFO @ Sat, 11 Dec 2021 06:51:05: 7000000 INFO @ Sat, 11 Dec 2021 06:51:06: 12000000 INFO @ Sat, 11 Dec 2021 06:51:07: 3000000 INFO @ Sat, 11 Dec 2021 06:51:12: 8000000 INFO @ Sat, 11 Dec 2021 06:51:13: 13000000 INFO @ Sat, 11 Dec 2021 06:51:14: 4000000 INFO @ Sat, 11 Dec 2021 06:51:19: 9000000 INFO @ Sat, 11 Dec 2021 06:51:20: 14000000 INFO @ Sat, 11 Dec 2021 06:51:22: 5000000 INFO @ Sat, 11 Dec 2021 06:51:26: 10000000 INFO @ Sat, 11 Dec 2021 06:51:27: 15000000 INFO @ Sat, 11 Dec 2021 06:51:29: 6000000 INFO @ Sat, 11 Dec 2021 06:51:34: 11000000 INFO @ Sat, 11 Dec 2021 06:51:35: 16000000 INFO @ Sat, 11 Dec 2021 06:51:36: 7000000 INFO @ Sat, 11 Dec 2021 06:51:41: 12000000 INFO @ Sat, 11 Dec 2021 06:51:42: 17000000 INFO @ Sat, 11 Dec 2021 06:51:44: 8000000 INFO @ Sat, 11 Dec 2021 06:51:48: 13000000 INFO @ Sat, 11 Dec 2021 06:51:49: 18000000 INFO @ Sat, 11 Dec 2021 06:51:51: 9000000 INFO @ Sat, 11 Dec 2021 06:51:55: 14000000 INFO @ Sat, 11 Dec 2021 06:51:56: 19000000 INFO @ Sat, 11 Dec 2021 06:51:58: 10000000 INFO @ Sat, 11 Dec 2021 06:52:03: 15000000 INFO @ Sat, 11 Dec 2021 06:52:03: 20000000 INFO @ Sat, 11 Dec 2021 06:52:06: 11000000 INFO @ Sat, 11 Dec 2021 06:52:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:52:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:52:06: #1 total tags in treatment: 20331079 INFO @ Sat, 11 Dec 2021 06:52:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:06: #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 06:52:06: #1 tags after filtering in treatment: 20331079 INFO @ Sat, 11 Dec 2021 06:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:06: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:08: #2 number of paired peaks: 145 WARNING @ Sat, 11 Dec 2021 06:52:08: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 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 44 bps INFO @ Sat, 11 Dec 2021 06:52:08: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.05_model.r WARNING @ Sat, 11 Dec 2021 06:52:08: #2 Since the d (44) 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): 44 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 06:52:10: 16000000 INFO @ Sat, 11 Dec 2021 06:52:13: 12000000 INFO @ Sat, 11 Dec 2021 06:52:17: 17000000 INFO @ Sat, 11 Dec 2021 06:52:20: 13000000 INFO @ Sat, 11 Dec 2021 06:52:23: 18000000 INFO @ Sat, 11 Dec 2021 06:52:27: 14000000 INFO @ Sat, 11 Dec 2021 06:52:30: 19000000 INFO @ Sat, 11 Dec 2021 06:52:33: 15000000 INFO @ Sat, 11 Dec 2021 06:52:37: 20000000 INFO @ Sat, 11 Dec 2021 06:52:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:52:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:52:40: #1 total tags in treatment: 20331079 INFO @ Sat, 11 Dec 2021 06:52:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:40: #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 06:52:40: #1 tags after filtering in treatment: 20331079 INFO @ Sat, 11 Dec 2021 06:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:40: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:40: 16000000 INFO @ Sat, 11 Dec 2021 06:52:41: #2 number of paired peaks: 145 WARNING @ Sat, 11 Dec 2021 06:52:41: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:41: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:41: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:41: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:41: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:41: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 06:52:41: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.10_model.r WARNING @ Sat, 11 Dec 2021 06:52:41: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:52:41: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 11 Dec 2021 06:52:41: #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 06:52:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:52:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:52:46: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:52:53: 18000000 INFO @ Sat, 11 Dec 2021 06:52:59: 19000000 INFO @ Sat, 11 Dec 2021 06:53:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.05_summits.bed INFO @ Sat, 11 Dec 2021 06:53:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2543 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:53:05: 20000000 INFO @ Sat, 11 Dec 2021 06:53:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:53:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:53:07: #1 total tags in treatment: 20331079 INFO @ Sat, 11 Dec 2021 06:53:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:53:07: #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 06:53:08: #1 tags after filtering in treatment: 20331079 INFO @ Sat, 11 Dec 2021 06:53:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:53:08: #1 finished! INFO @ Sat, 11 Dec 2021 06:53:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:53:09: #2 number of paired peaks: 145 WARNING @ Sat, 11 Dec 2021 06:53:09: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sat, 11 Dec 2021 06:53:09: start model_add_line... INFO @ Sat, 11 Dec 2021 06:53:09: start X-correlation... INFO @ Sat, 11 Dec 2021 06:53:09: end of X-cor INFO @ Sat, 11 Dec 2021 06:53:09: #2 finished! INFO @ Sat, 11 Dec 2021 06:53:09: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 06:53:09: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:53:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.20_model.r WARNING @ Sat, 11 Dec 2021 06:53:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:53:09: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 11 Dec 2021 06:53:09: #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 06:53:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:53:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:53:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.10_summits.bed INFO @ Sat, 11 Dec 2021 06:53:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1513 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:53:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689008/SRX8689008.20_summits.bed INFO @ Sat, 11 Dec 2021 06:54:02: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1092 records, 4 fields): 3 millis CompletedMACS2peakCalling