Job ID = 14172453 SRX = SRX10661194 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24742166 spots for SRR14305665/SRR14305665.sra Written 24742166 spots for SRR14305665/SRR14305665.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172918 ("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: 00:08:42 24742166 reads; of these: 24742166 (100.00%) were unpaired; of these: 1055552 (4.27%) aligned 0 times 14635753 (59.15%) aligned exactly 1 time 9050861 (36.58%) aligned >1 times 95.73% overall alignment rate Time searching: 00:08:42 Overall time: 00:08:42 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 8 files... [bam_rmdupse_core] 4985376 / 23686614 = 0.2105 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 15:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.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 15:43:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:43:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:43:58: 1000000 INFO @ Sat, 11 Dec 2021 15:44:04: 2000000 INFO @ Sat, 11 Dec 2021 15:44:11: 3000000 INFO @ Sat, 11 Dec 2021 15:44:17: 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 15:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.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 15:44:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:44:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:44:24: 5000000 INFO @ Sat, 11 Dec 2021 15:44:28: 1000000 INFO @ Sat, 11 Dec 2021 15:44:31: 6000000 INFO @ Sat, 11 Dec 2021 15:44:34: 2000000 INFO @ Sat, 11 Dec 2021 15:44:37: 7000000 INFO @ Sat, 11 Dec 2021 15:44:40: 3000000 INFO @ Sat, 11 Dec 2021 15:44:44: 8000000 INFO @ Sat, 11 Dec 2021 15:44:45: 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 @ Sat, 11 Dec 2021 15:44:51: 9000000 INFO @ Sat, 11 Dec 2021 15:44:51: 5000000 INFO @ Sat, 11 Dec 2021 15:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.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 15:44:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:44:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:44:57: 6000000 INFO @ Sat, 11 Dec 2021 15:44:57: 10000000 INFO @ Sat, 11 Dec 2021 15:44:58: 1000000 INFO @ Sat, 11 Dec 2021 15:45:02: 7000000 INFO @ Sat, 11 Dec 2021 15:45:04: 11000000 INFO @ Sat, 11 Dec 2021 15:45:04: 2000000 INFO @ Sat, 11 Dec 2021 15:45:08: 8000000 INFO @ Sat, 11 Dec 2021 15:45:10: 3000000 INFO @ Sat, 11 Dec 2021 15:45:10: 12000000 INFO @ Sat, 11 Dec 2021 15:45:13: 9000000 INFO @ Sat, 11 Dec 2021 15:45:16: 4000000 INFO @ Sat, 11 Dec 2021 15:45:17: 13000000 INFO @ Sat, 11 Dec 2021 15:45:19: 10000000 INFO @ Sat, 11 Dec 2021 15:45:22: 5000000 INFO @ Sat, 11 Dec 2021 15:45:24: 14000000 INFO @ Sat, 11 Dec 2021 15:45:25: 11000000 INFO @ Sat, 11 Dec 2021 15:45:28: 6000000 INFO @ Sat, 11 Dec 2021 15:45:30: 12000000 INFO @ Sat, 11 Dec 2021 15:45:31: 15000000 INFO @ Sat, 11 Dec 2021 15:45:34: 7000000 INFO @ Sat, 11 Dec 2021 15:45:36: 13000000 INFO @ Sat, 11 Dec 2021 15:45:39: 16000000 INFO @ Sat, 11 Dec 2021 15:45:40: 8000000 INFO @ Sat, 11 Dec 2021 15:45:42: 14000000 INFO @ Sat, 11 Dec 2021 15:45:46: 9000000 INFO @ Sat, 11 Dec 2021 15:45:46: 17000000 INFO @ Sat, 11 Dec 2021 15:45:47: 15000000 INFO @ Sat, 11 Dec 2021 15:45:52: 10000000 INFO @ Sat, 11 Dec 2021 15:45:53: 16000000 INFO @ Sat, 11 Dec 2021 15:45:54: 18000000 INFO @ Sat, 11 Dec 2021 15:45:58: 17000000 INFO @ Sat, 11 Dec 2021 15:45:58: 11000000 INFO @ Sat, 11 Dec 2021 15:46:00: #1 tag size is determined as 36 bps INFO @ Sat, 11 Dec 2021 15:46:00: #1 tag size = 36 INFO @ Sat, 11 Dec 2021 15:46:00: #1 total tags in treatment: 18701238 INFO @ Sat, 11 Dec 2021 15:46:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:46:00: #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 15:46:00: #1 tags after filtering in treatment: 18701238 INFO @ Sat, 11 Dec 2021 15:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:46:00: #1 finished! INFO @ Sat, 11 Dec 2021 15:46:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:46:02: #2 number of paired peaks: 324 WARNING @ Sat, 11 Dec 2021 15:46:02: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 11 Dec 2021 15:46:02: start model_add_line... INFO @ Sat, 11 Dec 2021 15:46:02: start X-correlation... INFO @ Sat, 11 Dec 2021 15:46:02: end of X-cor INFO @ Sat, 11 Dec 2021 15:46:02: #2 finished! INFO @ Sat, 11 Dec 2021 15:46:02: #2 predicted fragment length is 40 bps INFO @ Sat, 11 Dec 2021 15:46:02: #2 alternative fragment length(s) may be 2,40 bps INFO @ Sat, 11 Dec 2021 15:46:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.05_model.r WARNING @ Sat, 11 Dec 2021 15:46:02: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:46:02: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Sat, 11 Dec 2021 15:46:02: #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 15:46:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:46:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:46:03: 18000000 INFO @ Sat, 11 Dec 2021 15:46:04: 12000000 INFO @ Sat, 11 Dec 2021 15:46:07: #1 tag size is determined as 36 bps INFO @ Sat, 11 Dec 2021 15:46:07: #1 tag size = 36 INFO @ Sat, 11 Dec 2021 15:46:07: #1 total tags in treatment: 18701238 INFO @ Sat, 11 Dec 2021 15:46:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:46:07: #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 15:46:08: #1 tags after filtering in treatment: 18701238 INFO @ Sat, 11 Dec 2021 15:46:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:46:08: #1 finished! INFO @ Sat, 11 Dec 2021 15:46:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:46:09: #2 number of paired peaks: 324 WARNING @ Sat, 11 Dec 2021 15:46:09: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 11 Dec 2021 15:46:09: start model_add_line... INFO @ Sat, 11 Dec 2021 15:46:09: start X-correlation... INFO @ Sat, 11 Dec 2021 15:46:09: end of X-cor INFO @ Sat, 11 Dec 2021 15:46:09: #2 finished! INFO @ Sat, 11 Dec 2021 15:46:09: #2 predicted fragment length is 40 bps INFO @ Sat, 11 Dec 2021 15:46:09: #2 alternative fragment length(s) may be 2,40 bps INFO @ Sat, 11 Dec 2021 15:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.10_model.r WARNING @ Sat, 11 Dec 2021 15:46:09: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:46:09: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Sat, 11 Dec 2021 15:46:09: #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 15:46:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:46:09: 13000000 INFO @ Sat, 11 Dec 2021 15:46:15: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:46:21: 15000000 INFO @ Sat, 11 Dec 2021 15:46:27: 16000000 INFO @ Sat, 11 Dec 2021 15:46:33: 17000000 INFO @ Sat, 11 Dec 2021 15:46:38: 18000000 INFO @ Sat, 11 Dec 2021 15:46:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:46:42: #1 tag size is determined as 36 bps INFO @ Sat, 11 Dec 2021 15:46:42: #1 tag size = 36 INFO @ Sat, 11 Dec 2021 15:46:42: #1 total tags in treatment: 18701238 INFO @ Sat, 11 Dec 2021 15:46:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:46:42: #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 15:46:42: #1 tags after filtering in treatment: 18701238 INFO @ Sat, 11 Dec 2021 15:46:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:46:42: #1 finished! INFO @ Sat, 11 Dec 2021 15:46:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:46:43: #2 number of paired peaks: 324 WARNING @ Sat, 11 Dec 2021 15:46:43: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 11 Dec 2021 15:46:43: start model_add_line... INFO @ Sat, 11 Dec 2021 15:46:44: start X-correlation... INFO @ Sat, 11 Dec 2021 15:46:44: end of X-cor INFO @ Sat, 11 Dec 2021 15:46:44: #2 finished! INFO @ Sat, 11 Dec 2021 15:46:44: #2 predicted fragment length is 40 bps INFO @ Sat, 11 Dec 2021 15:46:44: #2 alternative fragment length(s) may be 2,40 bps INFO @ Sat, 11 Dec 2021 15:46:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.20_model.r WARNING @ Sat, 11 Dec 2021 15:46:44: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:46:44: #2 You may need to consider one of the other alternative d(s): 2,40 WARNING @ Sat, 11 Dec 2021 15:46:44: #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 15:46:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:46:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:46:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:47:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:47:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.05_summits.bed INFO @ Sat, 11 Dec 2021 15:47:01: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12083 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.10_summits.bed INFO @ Sat, 11 Dec 2021 15:47:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4055 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:47:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:47:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:47:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10661194/SRX10661194.20_summits.bed INFO @ Sat, 11 Dec 2021 15:47:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 1 millis CompletedMACS2peakCalling