Job ID = 14168016 SRX = SRX8688934 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:22 23264978 reads; of these: 23264978 (100.00%) were unpaired; of these: 799675 (3.44%) aligned 0 times 16225559 (69.74%) aligned exactly 1 time 6239744 (26.82%) aligned >1 times 96.56% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3090284 / 22465303 = 0.1376 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 14:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.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 14:35:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:35:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:35:51: 1000000 INFO @ Fri, 10 Dec 2021 14:36:00: 2000000 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 14:36:09: 3000000 INFO @ Fri, 10 Dec 2021 14:36:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.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 14:36:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:36:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:36:17: 4000000 INFO @ Fri, 10 Dec 2021 14:36:22: 1000000 INFO @ Fri, 10 Dec 2021 14:36:27: 5000000 INFO @ Fri, 10 Dec 2021 14:36:34: 2000000 INFO @ Fri, 10 Dec 2021 14:36:36: 6000000 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 14:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.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 14:36:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:36:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:36:44: 3000000 INFO @ Fri, 10 Dec 2021 14:36:47: 7000000 INFO @ Fri, 10 Dec 2021 14:36:54: 1000000 INFO @ Fri, 10 Dec 2021 14:36:55: 4000000 INFO @ Fri, 10 Dec 2021 14:36:59: 8000000 INFO @ Fri, 10 Dec 2021 14:37:04: 2000000 INFO @ Fri, 10 Dec 2021 14:37:05: 5000000 INFO @ Fri, 10 Dec 2021 14:37:10: 9000000 INFO @ Fri, 10 Dec 2021 14:37:14: 3000000 INFO @ Fri, 10 Dec 2021 14:37:14: 6000000 INFO @ Fri, 10 Dec 2021 14:37:21: 10000000 INFO @ Fri, 10 Dec 2021 14:37:22: 4000000 INFO @ Fri, 10 Dec 2021 14:37:24: 7000000 INFO @ Fri, 10 Dec 2021 14:37:31: 11000000 INFO @ Fri, 10 Dec 2021 14:37:32: 5000000 INFO @ Fri, 10 Dec 2021 14:37:34: 8000000 INFO @ Fri, 10 Dec 2021 14:37:41: 12000000 INFO @ Fri, 10 Dec 2021 14:37:41: 6000000 INFO @ Fri, 10 Dec 2021 14:37:43: 9000000 INFO @ Fri, 10 Dec 2021 14:37:51: 7000000 INFO @ Fri, 10 Dec 2021 14:37:52: 13000000 INFO @ Fri, 10 Dec 2021 14:37:53: 10000000 INFO @ Fri, 10 Dec 2021 14:38:02: 8000000 INFO @ Fri, 10 Dec 2021 14:38:03: 14000000 INFO @ Fri, 10 Dec 2021 14:38:04: 11000000 INFO @ Fri, 10 Dec 2021 14:38:12: 15000000 INFO @ Fri, 10 Dec 2021 14:38:13: 9000000 INFO @ Fri, 10 Dec 2021 14:38:14: 12000000 INFO @ Fri, 10 Dec 2021 14:38:23: 16000000 INFO @ Fri, 10 Dec 2021 14:38:24: 10000000 INFO @ Fri, 10 Dec 2021 14:38:26: 13000000 INFO @ Fri, 10 Dec 2021 14:38:32: 11000000 INFO @ Fri, 10 Dec 2021 14:38:32: 17000000 INFO @ Fri, 10 Dec 2021 14:38:36: 14000000 INFO @ Fri, 10 Dec 2021 14:38:41: 12000000 INFO @ Fri, 10 Dec 2021 14:38:41: 18000000 INFO @ Fri, 10 Dec 2021 14:38:46: 15000000 INFO @ Fri, 10 Dec 2021 14:38:50: 19000000 INFO @ Fri, 10 Dec 2021 14:38:50: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:38:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:38:54: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:38:54: #1 total tags in treatment: 19375019 INFO @ Fri, 10 Dec 2021 14:38:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:38:54: #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 14:38:55: #1 tags after filtering in treatment: 19374961 INFO @ Fri, 10 Dec 2021 14:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:38:55: #1 finished! INFO @ Fri, 10 Dec 2021 14:38:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:38:56: 16000000 INFO @ Fri, 10 Dec 2021 14:38:56: #2 number of paired peaks: 547 WARNING @ Fri, 10 Dec 2021 14:38:56: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Fri, 10 Dec 2021 14:38:56: start model_add_line... INFO @ Fri, 10 Dec 2021 14:38:57: start X-correlation... INFO @ Fri, 10 Dec 2021 14:38:57: end of X-cor INFO @ Fri, 10 Dec 2021 14:38:57: #2 finished! INFO @ Fri, 10 Dec 2021 14:38:57: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 14:38:57: #2 alternative fragment length(s) may be 2,46 bps INFO @ Fri, 10 Dec 2021 14:38:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.05_model.r WARNING @ Fri, 10 Dec 2021 14:38:57: #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 14:38:57: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Fri, 10 Dec 2021 14:38:57: #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 14:38:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:38:59: 14000000 INFO @ Fri, 10 Dec 2021 14:39:05: 17000000 INFO @ Fri, 10 Dec 2021 14:39:08: 15000000 INFO @ Fri, 10 Dec 2021 14:39:15: 18000000 INFO @ Fri, 10 Dec 2021 14:39:19: 16000000 INFO @ Fri, 10 Dec 2021 14:39:24: 19000000 INFO @ Fri, 10 Dec 2021 14:39:27: 17000000 INFO @ Fri, 10 Dec 2021 14:39:28: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:39:28: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:39:28: #1 total tags in treatment: 19375019 INFO @ Fri, 10 Dec 2021 14:39:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:39:28: #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 14:39:29: #1 tags after filtering in treatment: 19374961 INFO @ Fri, 10 Dec 2021 14:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:39:29: #1 finished! INFO @ Fri, 10 Dec 2021 14:39:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:39:30: #2 number of paired peaks: 547 WARNING @ Fri, 10 Dec 2021 14:39:30: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Fri, 10 Dec 2021 14:39:30: start model_add_line... INFO @ Fri, 10 Dec 2021 14:39:30: start X-correlation... INFO @ Fri, 10 Dec 2021 14:39:30: end of X-cor INFO @ Fri, 10 Dec 2021 14:39:30: #2 finished! INFO @ Fri, 10 Dec 2021 14:39:30: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 14:39:30: #2 alternative fragment length(s) may be 2,46 bps INFO @ Fri, 10 Dec 2021 14:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.10_model.r WARNING @ Fri, 10 Dec 2021 14:39:31: #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 14:39:31: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Fri, 10 Dec 2021 14:39:31: #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 14:39:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:39:35: 18000000 INFO @ Fri, 10 Dec 2021 14:39:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:39:43: 19000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:39:45: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:39:45: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:39:45: #1 total tags in treatment: 19375019 INFO @ Fri, 10 Dec 2021 14:39:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:39:45: #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 14:39:46: #1 tags after filtering in treatment: 19374961 INFO @ Fri, 10 Dec 2021 14:39:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:39:46: #1 finished! INFO @ Fri, 10 Dec 2021 14:39:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:39:49: #2 number of paired peaks: 547 WARNING @ Fri, 10 Dec 2021 14:39:49: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Fri, 10 Dec 2021 14:39:49: start model_add_line... INFO @ Fri, 10 Dec 2021 14:39:49: start X-correlation... INFO @ Fri, 10 Dec 2021 14:39:49: end of X-cor INFO @ Fri, 10 Dec 2021 14:39:49: #2 finished! INFO @ Fri, 10 Dec 2021 14:39:49: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 14:39:49: #2 alternative fragment length(s) may be 2,46 bps INFO @ Fri, 10 Dec 2021 14:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.20_model.r WARNING @ Fri, 10 Dec 2021 14:39:49: #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 14:39:49: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Fri, 10 Dec 2021 14:39:49: #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 14:39:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:40:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:40:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:40:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.05_summits.bed INFO @ Fri, 10 Dec 2021 14:40:05: Done! pass1 - making usageList (708 chroms): 30 millis pass2 - checking and writing primary data (3475 records, 4 fields): 346 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:40:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:40:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:40:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:40:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.10_summits.bed INFO @ Fri, 10 Dec 2021 14:40:37: Done! pass1 - making usageList (594 chroms): 17 millis pass2 - checking and writing primary data (2286 records, 4 fields): 878 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:40:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:41:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:41:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:41:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688934/SRX8688934.20_summits.bed INFO @ Fri, 10 Dec 2021 14:41:00: Done! pass1 - making usageList (321 chroms): 5 millis pass2 - checking and writing primary data (739 records, 4 fields): 11 millis CompletedMACS2peakCalling