Job ID = 16439006 SRX = SRX10031697 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: 00:11:25 30847229 reads; of these: 30847229 (100.00%) were unpaired; of these: 1019299 (3.30%) aligned 0 times 23280418 (75.47%) aligned exactly 1 time 6547512 (21.23%) aligned >1 times 96.70% overall alignment rate Time searching: 00:11:26 Overall time: 00:11:26 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] 7406523 / 29827930 = 0.2483 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 14:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.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 14:44:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:44:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:44:52: 1000000 INFO @ Tue, 02 Aug 2022 14:45:02: 2000000 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 14:45:12: 3000000 INFO @ Tue, 02 Aug 2022 14:45:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.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 14:45:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:45:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:45:22: 4000000 INFO @ Tue, 02 Aug 2022 14:45:23: 1000000 INFO @ Tue, 02 Aug 2022 14:45:32: 5000000 INFO @ Tue, 02 Aug 2022 14:45:32: 2000000 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 14:45:42: 3000000 INFO @ Tue, 02 Aug 2022 14:45:42: 6000000 INFO @ Tue, 02 Aug 2022 14:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.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 14:45:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:45:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:45:52: 4000000 INFO @ Tue, 02 Aug 2022 14:45:52: 7000000 INFO @ Tue, 02 Aug 2022 14:45:53: 1000000 INFO @ Tue, 02 Aug 2022 14:46:02: 5000000 INFO @ Tue, 02 Aug 2022 14:46:02: 8000000 INFO @ Tue, 02 Aug 2022 14:46:04: 2000000 INFO @ Tue, 02 Aug 2022 14:46:11: 6000000 INFO @ Tue, 02 Aug 2022 14:46:12: 9000000 INFO @ Tue, 02 Aug 2022 14:46:14: 3000000 INFO @ Tue, 02 Aug 2022 14:46:21: 7000000 INFO @ Tue, 02 Aug 2022 14:46:22: 10000000 INFO @ Tue, 02 Aug 2022 14:46:24: 4000000 INFO @ Tue, 02 Aug 2022 14:46:31: 8000000 INFO @ Tue, 02 Aug 2022 14:46:33: 11000000 INFO @ Tue, 02 Aug 2022 14:46:35: 5000000 INFO @ Tue, 02 Aug 2022 14:46:41: 9000000 INFO @ Tue, 02 Aug 2022 14:46:43: 12000000 INFO @ Tue, 02 Aug 2022 14:46:46: 6000000 INFO @ Tue, 02 Aug 2022 14:46:50: 10000000 INFO @ Tue, 02 Aug 2022 14:46:53: 13000000 INFO @ Tue, 02 Aug 2022 14:46:56: 7000000 INFO @ Tue, 02 Aug 2022 14:46:58: 11000000 INFO @ Tue, 02 Aug 2022 14:47:03: 14000000 INFO @ Tue, 02 Aug 2022 14:47:05: 12000000 INFO @ Tue, 02 Aug 2022 14:47:06: 8000000 INFO @ Tue, 02 Aug 2022 14:47:13: 15000000 INFO @ Tue, 02 Aug 2022 14:47:13: 13000000 INFO @ Tue, 02 Aug 2022 14:47:17: 9000000 INFO @ Tue, 02 Aug 2022 14:47:22: 14000000 INFO @ Tue, 02 Aug 2022 14:47:23: 16000000 INFO @ Tue, 02 Aug 2022 14:47:27: 10000000 INFO @ Tue, 02 Aug 2022 14:47:30: 15000000 INFO @ Tue, 02 Aug 2022 14:47:33: 17000000 INFO @ Tue, 02 Aug 2022 14:47:37: 11000000 INFO @ Tue, 02 Aug 2022 14:47:38: 16000000 INFO @ Tue, 02 Aug 2022 14:47:43: 18000000 INFO @ Tue, 02 Aug 2022 14:47:46: 17000000 INFO @ Tue, 02 Aug 2022 14:47:47: 12000000 INFO @ Tue, 02 Aug 2022 14:47:53: 19000000 INFO @ Tue, 02 Aug 2022 14:47:55: 18000000 INFO @ Tue, 02 Aug 2022 14:47:57: 13000000 INFO @ Tue, 02 Aug 2022 14:48:02: 20000000 INFO @ Tue, 02 Aug 2022 14:48:03: 19000000 INFO @ Tue, 02 Aug 2022 14:48:07: 14000000 INFO @ Tue, 02 Aug 2022 14:48:11: 20000000 INFO @ Tue, 02 Aug 2022 14:48:12: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:48:18: 15000000 INFO @ Tue, 02 Aug 2022 14:48:18: 21000000 INFO @ Tue, 02 Aug 2022 14:48:21: 22000000 INFO @ Tue, 02 Aug 2022 14:48:26: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:48:26: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:48:26: #1 total tags in treatment: 22421407 INFO @ Tue, 02 Aug 2022 14:48:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:26: #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 14:48:27: #1 tags after filtering in treatment: 22421378 INFO @ Tue, 02 Aug 2022 14:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:27: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:27: 22000000 INFO @ Tue, 02 Aug 2022 14:48:28: 16000000 INFO @ Tue, 02 Aug 2022 14:48:28: #2 number of paired peaks: 297 WARNING @ Tue, 02 Aug 2022 14:48:28: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 02 Aug 2022 14:48:28: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:28: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:28: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:28: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:28: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 14:48:28: #2 alternative fragment length(s) may be 2,71 bps INFO @ Tue, 02 Aug 2022 14:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.05_model.r WARNING @ Tue, 02 Aug 2022 14:48:28: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:48:28: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Tue, 02 Aug 2022 14:48:28: #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 14:48:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:48:31: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:48:31: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:48:31: #1 total tags in treatment: 22421407 INFO @ Tue, 02 Aug 2022 14:48:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:31: #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 14:48:32: #1 tags after filtering in treatment: 22421378 INFO @ Tue, 02 Aug 2022 14:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:32: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:33: #2 number of paired peaks: 297 WARNING @ Tue, 02 Aug 2022 14:48:33: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 02 Aug 2022 14:48:33: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:33: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:33: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:33: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:33: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 14:48:33: #2 alternative fragment length(s) may be 2,71 bps INFO @ Tue, 02 Aug 2022 14:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.10_model.r WARNING @ Tue, 02 Aug 2022 14:48:33: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:48:33: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Tue, 02 Aug 2022 14:48:33: #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 14:48:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:48:37: 17000000 INFO @ Tue, 02 Aug 2022 14:48:47: 18000000 INFO @ Tue, 02 Aug 2022 14:48:55: 19000000 INFO @ Tue, 02 Aug 2022 14:49:03: 20000000 INFO @ Tue, 02 Aug 2022 14:49:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:49:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:49:10: 21000000 INFO @ Tue, 02 Aug 2022 14:49:18: 22000000 INFO @ Tue, 02 Aug 2022 14:49:22: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:49:22: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:49:22: #1 total tags in treatment: 22421407 INFO @ Tue, 02 Aug 2022 14:49:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:22: #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 14:49:23: #1 tags after filtering in treatment: 22421378 INFO @ Tue, 02 Aug 2022 14:49:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:49:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:49:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.05_summits.bed INFO @ Tue, 02 Aug 2022 14:49:23: Done! pass1 - making usageList (542 chroms): 2 millis pass2 - checking and writing primary data (2963 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:49:24: #2 number of paired peaks: 297 WARNING @ Tue, 02 Aug 2022 14:49:24: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 02 Aug 2022 14:49:24: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:24: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:24: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:24: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:24: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 14:49:24: #2 alternative fragment length(s) may be 2,71 bps INFO @ Tue, 02 Aug 2022 14:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.20_model.r WARNING @ Tue, 02 Aug 2022 14:49:24: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:49:24: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Tue, 02 Aug 2022 14:49:24: #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 14:49:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.10_summits.bed INFO @ Tue, 02 Aug 2022 14:49:28: Done! pass1 - making usageList (425 chroms): 1 millis pass2 - checking and writing primary data (1590 records, 4 fields): 44 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:50:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031697/SRX10031697.20_summits.bed INFO @ Tue, 02 Aug 2022 14:50:20: Done! pass1 - making usageList (237 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 27 millis CompletedMACS2peakCalling