Job ID = 16439493 SRX = SRX13227889 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: 00:11:55 36353930 reads; of these: 36353930 (100.00%) were unpaired; of these: 1520254 (4.18%) aligned 0 times 26322120 (72.41%) aligned exactly 1 time 8511556 (23.41%) aligned >1 times 95.82% overall alignment rate Time searching: 00:11:55 Overall time: 00:11:55 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 16 files... [bam_rmdupse_core] 5626759 / 34833676 = 0.1615 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 15:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.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 15:41:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:41:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:41:31: 1000000 INFO @ Tue, 02 Aug 2022 15:41:37: 2000000 INFO @ Tue, 02 Aug 2022 15:41:43: 3000000 INFO @ Tue, 02 Aug 2022 15:41:49: 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 15:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.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 15:41:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:41:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:41:55: 5000000 INFO @ Tue, 02 Aug 2022 15:42:00: 1000000 INFO @ Tue, 02 Aug 2022 15:42:01: 6000000 INFO @ Tue, 02 Aug 2022 15:42:06: 2000000 INFO @ Tue, 02 Aug 2022 15:42:07: 7000000 INFO @ Tue, 02 Aug 2022 15:42:11: 3000000 INFO @ Tue, 02 Aug 2022 15:42:13: 8000000 INFO @ Tue, 02 Aug 2022 15:42:16: 4000000 INFO @ Tue, 02 Aug 2022 15:42:19: 9000000 INFO @ Tue, 02 Aug 2022 15:42:21: 5000000 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 15:42:25: 10000000 INFO @ Tue, 02 Aug 2022 15:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.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 15:42:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:42:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:42:26: 6000000 INFO @ Tue, 02 Aug 2022 15:42:31: 11000000 INFO @ Tue, 02 Aug 2022 15:42:31: 7000000 INFO @ Tue, 02 Aug 2022 15:42:32: 1000000 INFO @ Tue, 02 Aug 2022 15:42:37: 8000000 INFO @ Tue, 02 Aug 2022 15:42:37: 12000000 INFO @ Tue, 02 Aug 2022 15:42:37: 2000000 INFO @ Tue, 02 Aug 2022 15:42:42: 9000000 INFO @ Tue, 02 Aug 2022 15:42:42: 13000000 INFO @ Tue, 02 Aug 2022 15:42:43: 3000000 INFO @ Tue, 02 Aug 2022 15:42:47: 10000000 INFO @ Tue, 02 Aug 2022 15:42:48: 4000000 INFO @ Tue, 02 Aug 2022 15:42:48: 14000000 INFO @ Tue, 02 Aug 2022 15:42:53: 11000000 INFO @ Tue, 02 Aug 2022 15:42:54: 5000000 INFO @ Tue, 02 Aug 2022 15:42:54: 15000000 INFO @ Tue, 02 Aug 2022 15:42:58: 12000000 INFO @ Tue, 02 Aug 2022 15:42:59: 6000000 INFO @ Tue, 02 Aug 2022 15:43:00: 16000000 INFO @ Tue, 02 Aug 2022 15:43:04: 13000000 INFO @ Tue, 02 Aug 2022 15:43:04: 7000000 INFO @ Tue, 02 Aug 2022 15:43:06: 17000000 INFO @ Tue, 02 Aug 2022 15:43:09: 14000000 INFO @ Tue, 02 Aug 2022 15:43:10: 8000000 INFO @ Tue, 02 Aug 2022 15:43:12: 18000000 INFO @ Tue, 02 Aug 2022 15:43:14: 15000000 INFO @ Tue, 02 Aug 2022 15:43:15: 9000000 INFO @ Tue, 02 Aug 2022 15:43:18: 19000000 INFO @ Tue, 02 Aug 2022 15:43:20: 16000000 INFO @ Tue, 02 Aug 2022 15:43:21: 10000000 INFO @ Tue, 02 Aug 2022 15:43:24: 20000000 INFO @ Tue, 02 Aug 2022 15:43:25: 17000000 INFO @ Tue, 02 Aug 2022 15:43:26: 11000000 INFO @ Tue, 02 Aug 2022 15:43:30: 21000000 INFO @ Tue, 02 Aug 2022 15:43:31: 18000000 INFO @ Tue, 02 Aug 2022 15:43:32: 12000000 INFO @ Tue, 02 Aug 2022 15:43:36: 22000000 INFO @ Tue, 02 Aug 2022 15:43:36: 19000000 INFO @ Tue, 02 Aug 2022 15:43:38: 13000000 INFO @ Tue, 02 Aug 2022 15:43:41: 23000000 INFO @ Tue, 02 Aug 2022 15:43:42: 20000000 INFO @ Tue, 02 Aug 2022 15:43:44: 14000000 INFO @ Tue, 02 Aug 2022 15:43:47: 21000000 INFO @ Tue, 02 Aug 2022 15:43:48: 24000000 INFO @ Tue, 02 Aug 2022 15:43:49: 15000000 INFO @ Tue, 02 Aug 2022 15:43:53: 22000000 INFO @ Tue, 02 Aug 2022 15:43:54: 25000000 INFO @ Tue, 02 Aug 2022 15:43:55: 16000000 INFO @ Tue, 02 Aug 2022 15:43:59: 23000000 INFO @ Tue, 02 Aug 2022 15:44:00: 26000000 INFO @ Tue, 02 Aug 2022 15:44:01: 17000000 INFO @ Tue, 02 Aug 2022 15:44:05: 24000000 INFO @ Tue, 02 Aug 2022 15:44:06: 18000000 INFO @ Tue, 02 Aug 2022 15:44:07: 27000000 INFO @ Tue, 02 Aug 2022 15:44:10: 25000000 INFO @ Tue, 02 Aug 2022 15:44:12: 19000000 INFO @ Tue, 02 Aug 2022 15:44:13: 28000000 INFO @ Tue, 02 Aug 2022 15:44:15: 26000000 INFO @ Tue, 02 Aug 2022 15:44:17: 20000000 INFO @ Tue, 02 Aug 2022 15:44:19: 29000000 INFO @ Tue, 02 Aug 2022 15:44:21: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:44:21: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:44:21: #1 total tags in treatment: 29206917 INFO @ Tue, 02 Aug 2022 15:44:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:44:21: #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 15:44:21: 27000000 INFO @ Tue, 02 Aug 2022 15:44:21: #1 tags after filtering in treatment: 29206917 INFO @ Tue, 02 Aug 2022 15:44:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:44:21: #1 finished! INFO @ Tue, 02 Aug 2022 15:44:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:44:23: 21000000 INFO @ Tue, 02 Aug 2022 15:44:23: #2 number of paired peaks: 208 WARNING @ Tue, 02 Aug 2022 15:44:23: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 02 Aug 2022 15:44:23: start model_add_line... INFO @ Tue, 02 Aug 2022 15:44:23: start X-correlation... INFO @ Tue, 02 Aug 2022 15:44:24: end of X-cor INFO @ Tue, 02 Aug 2022 15:44:24: #2 finished! INFO @ Tue, 02 Aug 2022 15:44:24: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 15:44:24: #2 alternative fragment length(s) may be 3,69 bps INFO @ Tue, 02 Aug 2022 15:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.05_model.r WARNING @ Tue, 02 Aug 2022 15:44:24: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:44:24: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Tue, 02 Aug 2022 15:44:24: #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 15:44:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:44:26: 28000000 INFO @ Tue, 02 Aug 2022 15:44:28: 22000000 INFO @ Tue, 02 Aug 2022 15:44:31: 29000000 INFO @ Tue, 02 Aug 2022 15:44:33: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:44:33: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:44:33: #1 total tags in treatment: 29206917 INFO @ Tue, 02 Aug 2022 15:44:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:44:33: #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 15:44:34: #1 tags after filtering in treatment: 29206917 INFO @ Tue, 02 Aug 2022 15:44:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:44:34: #1 finished! INFO @ Tue, 02 Aug 2022 15:44:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:44:34: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:44:35: #2 number of paired peaks: 208 WARNING @ Tue, 02 Aug 2022 15:44:35: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 02 Aug 2022 15:44:35: start model_add_line... INFO @ Tue, 02 Aug 2022 15:44:35: start X-correlation... INFO @ Tue, 02 Aug 2022 15:44:35: end of X-cor INFO @ Tue, 02 Aug 2022 15:44:35: #2 finished! INFO @ Tue, 02 Aug 2022 15:44:35: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 15:44:35: #2 alternative fragment length(s) may be 3,69 bps INFO @ Tue, 02 Aug 2022 15:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.10_model.r WARNING @ Tue, 02 Aug 2022 15:44:36: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:44:36: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Tue, 02 Aug 2022 15:44:36: #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 15:44:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:44:39: 24000000 INFO @ Tue, 02 Aug 2022 15:44:45: 25000000 INFO @ Tue, 02 Aug 2022 15:44:50: 26000000 INFO @ Tue, 02 Aug 2022 15:44:55: 27000000 INFO @ Tue, 02 Aug 2022 15:45:00: 28000000 INFO @ Tue, 02 Aug 2022 15:45:05: 29000000 INFO @ Tue, 02 Aug 2022 15:45:07: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:45:07: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:45:07: #1 total tags in treatment: 29206917 INFO @ Tue, 02 Aug 2022 15:45:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:45:07: #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 15:45:07: #1 tags after filtering in treatment: 29206917 INFO @ Tue, 02 Aug 2022 15:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:45:07: #1 finished! INFO @ Tue, 02 Aug 2022 15:45:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:45:09: #2 number of paired peaks: 208 WARNING @ Tue, 02 Aug 2022 15:45:09: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 02 Aug 2022 15:45:09: start model_add_line... INFO @ Tue, 02 Aug 2022 15:45:09: start X-correlation... INFO @ Tue, 02 Aug 2022 15:45:09: end of X-cor INFO @ Tue, 02 Aug 2022 15:45:09: #2 finished! INFO @ Tue, 02 Aug 2022 15:45:09: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 15:45:09: #2 alternative fragment length(s) may be 3,69 bps INFO @ Tue, 02 Aug 2022 15:45:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.20_model.r WARNING @ Tue, 02 Aug 2022 15:45:09: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:45:09: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Tue, 02 Aug 2022 15:45:09: #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 15:45:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:45:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:45:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:45:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:45:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:45:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.05_summits.bed INFO @ Tue, 02 Aug 2022 15:45:32: Done! pass1 - making usageList (689 chroms): 2 millis pass2 - checking and writing primary data (5611 records, 4 fields): 57 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.10_summits.bed INFO @ Tue, 02 Aug 2022 15:45:43: Done! pass1 - making usageList (607 chroms): 1 millis pass2 - checking and writing primary data (2550 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:45:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227889/SRX13227889.20_summits.bed INFO @ Tue, 02 Aug 2022 15:46:17: Done! pass1 - making usageList (454 chroms): 2 millis pass2 - checking and writing primary data (1252 records, 4 fields): 35 millis CompletedMACS2peakCalling