Job ID = 14168088 SRX = SRX8723971 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22756793 spots for SRR12213379/SRR12213379.sra Written 22756793 spots for SRR12213379/SRR12213379.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168856 ("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: 00:08:46 22756793 reads; of these: 22756793 (100.00%) were unpaired; of these: 1714623 (7.53%) aligned 0 times 15322028 (67.33%) aligned exactly 1 time 5720142 (25.14%) aligned >1 times 92.47% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 3735116 / 21042170 = 0.1775 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 15:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.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 15:27:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:27:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:27:43: 1000000 INFO @ Fri, 10 Dec 2021 15:27:50: 2000000 INFO @ Fri, 10 Dec 2021 15:27:57: 3000000 INFO @ Fri, 10 Dec 2021 15:28:04: 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 @ Fri, 10 Dec 2021 15:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.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 15:28:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:28:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:28:11: 5000000 INFO @ Fri, 10 Dec 2021 15:28:14: 1000000 INFO @ Fri, 10 Dec 2021 15:28:18: 6000000 INFO @ Fri, 10 Dec 2021 15:28:20: 2000000 INFO @ Fri, 10 Dec 2021 15:28:25: 7000000 INFO @ Fri, 10 Dec 2021 15:28:27: 3000000 INFO @ Fri, 10 Dec 2021 15:28:32: 8000000 INFO @ Fri, 10 Dec 2021 15:28:34: 4000000 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 15:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.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 15:28:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:28:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:28:39: 9000000 INFO @ Fri, 10 Dec 2021 15:28:40: 5000000 INFO @ Fri, 10 Dec 2021 15:28:44: 1000000 INFO @ Fri, 10 Dec 2021 15:28:46: 10000000 INFO @ Fri, 10 Dec 2021 15:28:47: 6000000 INFO @ Fri, 10 Dec 2021 15:28:51: 2000000 INFO @ Fri, 10 Dec 2021 15:28:53: 11000000 INFO @ Fri, 10 Dec 2021 15:28:54: 7000000 INFO @ Fri, 10 Dec 2021 15:28:58: 3000000 INFO @ Fri, 10 Dec 2021 15:29:00: 12000000 INFO @ Fri, 10 Dec 2021 15:29:00: 8000000 INFO @ Fri, 10 Dec 2021 15:29:05: 4000000 INFO @ Fri, 10 Dec 2021 15:29:07: 9000000 INFO @ Fri, 10 Dec 2021 15:29:07: 13000000 INFO @ Fri, 10 Dec 2021 15:29:13: 5000000 INFO @ Fri, 10 Dec 2021 15:29:14: 10000000 INFO @ Fri, 10 Dec 2021 15:29:14: 14000000 INFO @ Fri, 10 Dec 2021 15:29:20: 6000000 INFO @ Fri, 10 Dec 2021 15:29:20: 11000000 INFO @ Fri, 10 Dec 2021 15:29:22: 15000000 INFO @ Fri, 10 Dec 2021 15:29:27: 12000000 INFO @ Fri, 10 Dec 2021 15:29:27: 7000000 INFO @ Fri, 10 Dec 2021 15:29:29: 16000000 INFO @ Fri, 10 Dec 2021 15:29:34: 13000000 INFO @ Fri, 10 Dec 2021 15:29:34: 8000000 INFO @ Fri, 10 Dec 2021 15:29:37: 17000000 INFO @ Fri, 10 Dec 2021 15:29:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:29:39: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:29:39: #1 total tags in treatment: 17307054 INFO @ Fri, 10 Dec 2021 15:29:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:29:39: #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 15:29:39: #1 tags after filtering in treatment: 17307054 INFO @ Fri, 10 Dec 2021 15:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:29:39: #1 finished! INFO @ Fri, 10 Dec 2021 15:29:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:29:40: #2 number of paired peaks: 174 WARNING @ Fri, 10 Dec 2021 15:29:40: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 10 Dec 2021 15:29:40: start model_add_line... INFO @ Fri, 10 Dec 2021 15:29:40: start X-correlation... INFO @ Fri, 10 Dec 2021 15:29:40: end of X-cor INFO @ Fri, 10 Dec 2021 15:29:40: #2 finished! INFO @ Fri, 10 Dec 2021 15:29:40: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 15:29:40: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 15:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.05_model.r WARNING @ Fri, 10 Dec 2021 15:29:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:29:40: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 15:29:40: #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 15:29:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:29:41: 14000000 INFO @ Fri, 10 Dec 2021 15:29:41: 9000000 INFO @ Fri, 10 Dec 2021 15:29:48: 15000000 INFO @ Fri, 10 Dec 2021 15:29:48: 10000000 INFO @ Fri, 10 Dec 2021 15:29:55: 16000000 INFO @ Fri, 10 Dec 2021 15:29:55: 11000000 INFO @ Fri, 10 Dec 2021 15:30:02: 17000000 INFO @ Fri, 10 Dec 2021 15:30:03: 12000000 INFO @ Fri, 10 Dec 2021 15:30:04: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:30:04: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:30:04: #1 total tags in treatment: 17307054 INFO @ Fri, 10 Dec 2021 15:30:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:30:04: #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 15:30:04: #1 tags after filtering in treatment: 17307054 INFO @ Fri, 10 Dec 2021 15:30:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:30:04: #1 finished! INFO @ Fri, 10 Dec 2021 15:30:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:30:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:30:05: #2 number of paired peaks: 174 WARNING @ Fri, 10 Dec 2021 15:30:05: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 10 Dec 2021 15:30:05: start model_add_line... INFO @ Fri, 10 Dec 2021 15:30:05: start X-correlation... INFO @ Fri, 10 Dec 2021 15:30:05: end of X-cor INFO @ Fri, 10 Dec 2021 15:30:05: #2 finished! INFO @ Fri, 10 Dec 2021 15:30:05: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 15:30:05: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 15:30:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.10_model.r WARNING @ Fri, 10 Dec 2021 15:30:05: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:30:05: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 15:30:05: #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 15:30:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:30:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:30:10: 13000000 INFO @ Fri, 10 Dec 2021 15:30:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:30:16: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:30:23: 15000000 INFO @ Fri, 10 Dec 2021 15:30:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.05_summits.bed INFO @ Fri, 10 Dec 2021 15:30:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2105 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:30:30: 16000000 INFO @ Fri, 10 Dec 2021 15:30:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:30:37: 17000000 INFO @ Fri, 10 Dec 2021 15:30:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:30:39: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:30:39: #1 total tags in treatment: 17307054 INFO @ Fri, 10 Dec 2021 15:30:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:30:39: #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 15:30:39: #1 tags after filtering in treatment: 17307054 INFO @ Fri, 10 Dec 2021 15:30:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:30:39: #1 finished! INFO @ Fri, 10 Dec 2021 15:30:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:30:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:30:40: #2 number of paired peaks: 174 WARNING @ Fri, 10 Dec 2021 15:30:40: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 10 Dec 2021 15:30:40: start model_add_line... INFO @ Fri, 10 Dec 2021 15:30:40: start X-correlation... INFO @ Fri, 10 Dec 2021 15:30:40: end of X-cor INFO @ Fri, 10 Dec 2021 15:30:40: #2 finished! INFO @ Fri, 10 Dec 2021 15:30:40: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 15:30:40: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 15:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.20_model.r WARNING @ Fri, 10 Dec 2021 15:30:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:30:40: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 15:30:40: #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 15:30:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:30:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:30:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.10_summits.bed INFO @ Fri, 10 Dec 2021 15:30:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1483 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:31:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:31:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:31:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:31:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723971/SRX8723971.20_summits.bed INFO @ Fri, 10 Dec 2021 15:31:27: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (1004 records, 4 fields): 4 millis CompletedMACS2peakCalling