Job ID = 16438043 SRX = SRX12261347 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23430749 spots for SRR15972603/SRR15972603.sra Written 23430749 spots for SRR15972603/SRR15972603.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438128 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:04 23430749 reads; of these: 23430749 (100.00%) were unpaired; of these: 707771 (3.02%) aligned 0 times 13556361 (57.86%) aligned exactly 1 time 9166617 (39.12%) aligned >1 times 96.98% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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] 8865655 / 22722978 = 0.3902 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.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 @ Tue, 02 Aug 2022 13:43:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:43:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:43:24: 1000000 INFO @ Tue, 02 Aug 2022 13:43:30: 2000000 INFO @ Tue, 02 Aug 2022 13:43:36: 3000000 INFO @ Tue, 02 Aug 2022 13:43:42: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:43:48: 5000000 INFO @ Tue, 02 Aug 2022 13:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.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 @ Tue, 02 Aug 2022 13:43:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:43:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:43:54: 6000000 INFO @ Tue, 02 Aug 2022 13:43:55: 1000000 INFO @ Tue, 02 Aug 2022 13:44:00: 7000000 INFO @ Tue, 02 Aug 2022 13:44:01: 2000000 INFO @ Tue, 02 Aug 2022 13:44:05: 8000000 INFO @ Tue, 02 Aug 2022 13:44:07: 3000000 INFO @ Tue, 02 Aug 2022 13:44:11: 9000000 INFO @ Tue, 02 Aug 2022 13:44:13: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:44:17: 10000000 INFO @ Tue, 02 Aug 2022 13:44:19: 5000000 INFO @ Tue, 02 Aug 2022 13:44:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.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 @ Tue, 02 Aug 2022 13:44:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:44:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:44:24: 11000000 INFO @ Tue, 02 Aug 2022 13:44:25: 6000000 INFO @ Tue, 02 Aug 2022 13:44:27: 1000000 INFO @ Tue, 02 Aug 2022 13:44:30: 12000000 INFO @ Tue, 02 Aug 2022 13:44:31: 7000000 INFO @ Tue, 02 Aug 2022 13:44:33: 2000000 INFO @ Tue, 02 Aug 2022 13:44:36: 13000000 INFO @ Tue, 02 Aug 2022 13:44:37: 8000000 INFO @ Tue, 02 Aug 2022 13:44:40: 3000000 INFO @ Tue, 02 Aug 2022 13:44:41: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:44:41: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:44:41: #1 total tags in treatment: 13857323 INFO @ Tue, 02 Aug 2022 13:44:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:44:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:44:41: #1 tags after filtering in treatment: 13857323 INFO @ Tue, 02 Aug 2022 13:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:44:41: #1 finished! INFO @ Tue, 02 Aug 2022 13:44:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:44:42: #2 number of paired peaks: 171 WARNING @ Tue, 02 Aug 2022 13:44:42: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 02 Aug 2022 13:44:42: start model_add_line... INFO @ Tue, 02 Aug 2022 13:44:43: start X-correlation... INFO @ Tue, 02 Aug 2022 13:44:43: end of X-cor INFO @ Tue, 02 Aug 2022 13:44:43: #2 finished! INFO @ Tue, 02 Aug 2022 13:44:43: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:44:43: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.05_model.r WARNING @ Tue, 02 Aug 2022 13:44:43: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:44:43: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:44:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:44:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:44:44: 9000000 INFO @ Tue, 02 Aug 2022 13:44:46: 4000000 INFO @ Tue, 02 Aug 2022 13:44:50: 10000000 INFO @ Tue, 02 Aug 2022 13:44:52: 5000000 INFO @ Tue, 02 Aug 2022 13:44:56: 11000000 INFO @ Tue, 02 Aug 2022 13:44:59: 6000000 INFO @ Tue, 02 Aug 2022 13:45:02: 12000000 INFO @ Tue, 02 Aug 2022 13:45:05: 7000000 INFO @ Tue, 02 Aug 2022 13:45:08: 13000000 INFO @ Tue, 02 Aug 2022 13:45:11: 8000000 INFO @ Tue, 02 Aug 2022 13:45:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:45:13: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:45:13: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:45:13: #1 total tags in treatment: 13857323 INFO @ Tue, 02 Aug 2022 13:45:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:45:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:45:14: #1 tags after filtering in treatment: 13857323 INFO @ Tue, 02 Aug 2022 13:45:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:45:14: #1 finished! INFO @ Tue, 02 Aug 2022 13:45:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:45:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:45:15: #2 number of paired peaks: 171 WARNING @ Tue, 02 Aug 2022 13:45:15: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 02 Aug 2022 13:45:15: start model_add_line... INFO @ Tue, 02 Aug 2022 13:45:15: start X-correlation... INFO @ Tue, 02 Aug 2022 13:45:15: end of X-cor INFO @ Tue, 02 Aug 2022 13:45:15: #2 finished! INFO @ Tue, 02 Aug 2022 13:45:15: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:45:15: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:45:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.10_model.r WARNING @ Tue, 02 Aug 2022 13:45:15: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:45:15: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:45:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:45:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:45:17: 9000000 INFO @ Tue, 02 Aug 2022 13:45:23: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.05_summits.bed INFO @ Tue, 02 Aug 2022 13:45:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6680 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:45:28: 11000000 INFO @ Tue, 02 Aug 2022 13:45:34: 12000000 INFO @ Tue, 02 Aug 2022 13:45:40: 13000000 INFO @ Tue, 02 Aug 2022 13:45:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:45:45: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:45:45: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:45:45: #1 total tags in treatment: 13857323 INFO @ Tue, 02 Aug 2022 13:45:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:45:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:45:45: #1 tags after filtering in treatment: 13857323 INFO @ Tue, 02 Aug 2022 13:45:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:45:45: #1 finished! INFO @ Tue, 02 Aug 2022 13:45:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:45:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:45:46: #2 number of paired peaks: 171 WARNING @ Tue, 02 Aug 2022 13:45:46: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 02 Aug 2022 13:45:46: start model_add_line... INFO @ Tue, 02 Aug 2022 13:45:46: start X-correlation... INFO @ Tue, 02 Aug 2022 13:45:46: end of X-cor INFO @ Tue, 02 Aug 2022 13:45:46: #2 finished! INFO @ Tue, 02 Aug 2022 13:45:46: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:45:46: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:45:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.20_model.r WARNING @ Tue, 02 Aug 2022 13:45:46: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:45:46: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:45:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:45:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:45:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.10_summits.bed INFO @ Tue, 02 Aug 2022 13:45:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3206 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:46:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:46:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261347/SRX12261347.20_summits.bed INFO @ Tue, 02 Aug 2022 13:46:29: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1017 records, 4 fields): 21 millis CompletedMACS2peakCalling