Job ID = 14167520 SRX = SRX7723697 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: 00:09:05 27756323 reads; of these: 27756323 (100.00%) were unpaired; of these: 1904841 (6.86%) aligned 0 times 21309872 (76.77%) aligned exactly 1 time 4541610 (16.36%) aligned >1 times 93.14% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 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] 2657681 / 25851482 = 0.1028 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 12:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.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 12:46:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:46:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:47:00: 1000000 INFO @ Fri, 10 Dec 2021 12:47:06: 2000000 INFO @ Fri, 10 Dec 2021 12:47:11: 3000000 INFO @ Fri, 10 Dec 2021 12:47:17: 4000000 INFO @ Fri, 10 Dec 2021 12:47:22: 5000000 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 12:47:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.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 12:47:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:47:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:47:28: 6000000 INFO @ Fri, 10 Dec 2021 12:47:31: 1000000 INFO @ Fri, 10 Dec 2021 12:47:35: 7000000 INFO @ Fri, 10 Dec 2021 12:47:37: 2000000 INFO @ Fri, 10 Dec 2021 12:47:41: 8000000 INFO @ Fri, 10 Dec 2021 12:47:44: 3000000 INFO @ Fri, 10 Dec 2021 12:47:47: 9000000 INFO @ Fri, 10 Dec 2021 12:47:50: 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 @ Fri, 10 Dec 2021 12:47:53: 10000000 INFO @ Fri, 10 Dec 2021 12:47:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.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 12:47:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:47:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:47:56: 5000000 INFO @ Fri, 10 Dec 2021 12:48:00: 11000000 INFO @ Fri, 10 Dec 2021 12:48:01: 1000000 INFO @ Fri, 10 Dec 2021 12:48:02: 6000000 INFO @ Fri, 10 Dec 2021 12:48:06: 12000000 INFO @ Fri, 10 Dec 2021 12:48:07: 2000000 INFO @ Fri, 10 Dec 2021 12:48:08: 7000000 INFO @ Fri, 10 Dec 2021 12:48:12: 13000000 INFO @ Fri, 10 Dec 2021 12:48:13: 3000000 INFO @ Fri, 10 Dec 2021 12:48:14: 8000000 INFO @ Fri, 10 Dec 2021 12:48:18: 14000000 INFO @ Fri, 10 Dec 2021 12:48:19: 4000000 INFO @ Fri, 10 Dec 2021 12:48:20: 9000000 INFO @ Fri, 10 Dec 2021 12:48:24: 15000000 INFO @ Fri, 10 Dec 2021 12:48:25: 5000000 INFO @ Fri, 10 Dec 2021 12:48:27: 10000000 INFO @ Fri, 10 Dec 2021 12:48:30: 16000000 INFO @ Fri, 10 Dec 2021 12:48:31: 6000000 INFO @ Fri, 10 Dec 2021 12:48:33: 11000000 INFO @ Fri, 10 Dec 2021 12:48:36: 17000000 INFO @ Fri, 10 Dec 2021 12:48:37: 7000000 INFO @ Fri, 10 Dec 2021 12:48:39: 12000000 INFO @ Fri, 10 Dec 2021 12:48:42: 18000000 INFO @ Fri, 10 Dec 2021 12:48:43: 8000000 INFO @ Fri, 10 Dec 2021 12:48:45: 13000000 INFO @ Fri, 10 Dec 2021 12:48:49: 19000000 INFO @ Fri, 10 Dec 2021 12:48:50: 9000000 INFO @ Fri, 10 Dec 2021 12:48:51: 14000000 INFO @ Fri, 10 Dec 2021 12:48:55: 20000000 INFO @ Fri, 10 Dec 2021 12:48:56: 10000000 INFO @ Fri, 10 Dec 2021 12:48:57: 15000000 INFO @ Fri, 10 Dec 2021 12:49:01: 21000000 INFO @ Fri, 10 Dec 2021 12:49:02: 11000000 INFO @ Fri, 10 Dec 2021 12:49:03: 16000000 INFO @ Fri, 10 Dec 2021 12:49:07: 22000000 INFO @ Fri, 10 Dec 2021 12:49:08: 12000000 INFO @ Fri, 10 Dec 2021 12:49:09: 17000000 INFO @ Fri, 10 Dec 2021 12:49:13: 23000000 INFO @ Fri, 10 Dec 2021 12:49:14: 13000000 INFO @ Fri, 10 Dec 2021 12:49:14: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:49:14: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:49:14: #1 total tags in treatment: 23193801 INFO @ Fri, 10 Dec 2021 12:49:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:49:14: #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 12:49:15: #1 tags after filtering in treatment: 23193692 INFO @ Fri, 10 Dec 2021 12:49:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:49:15: #1 finished! INFO @ Fri, 10 Dec 2021 12:49:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:49:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:49:15: 18000000 INFO @ Fri, 10 Dec 2021 12:49:16: #2 number of paired peaks: 204 WARNING @ Fri, 10 Dec 2021 12:49:16: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Fri, 10 Dec 2021 12:49:16: start model_add_line... INFO @ Fri, 10 Dec 2021 12:49:17: start X-correlation... INFO @ Fri, 10 Dec 2021 12:49:17: end of X-cor INFO @ Fri, 10 Dec 2021 12:49:17: #2 finished! INFO @ Fri, 10 Dec 2021 12:49:17: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 12:49:17: #2 alternative fragment length(s) may be 2,66 bps INFO @ Fri, 10 Dec 2021 12:49:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05_model.r WARNING @ Fri, 10 Dec 2021 12:49:17: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:49:17: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Fri, 10 Dec 2021 12:49:17: #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 12:49:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:49:20: 14000000 INFO @ Fri, 10 Dec 2021 12:49:22: 19000000 INFO @ Fri, 10 Dec 2021 12:49:26: 15000000 INFO @ Fri, 10 Dec 2021 12:49:28: 20000000 INFO @ Fri, 10 Dec 2021 12:49:32: 16000000 INFO @ Fri, 10 Dec 2021 12:49:34: 21000000 INFO @ Fri, 10 Dec 2021 12:49:38: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:49:40: 22000000 INFO @ Fri, 10 Dec 2021 12:49:44: 18000000 INFO @ Fri, 10 Dec 2021 12:49:46: 23000000 INFO @ Fri, 10 Dec 2021 12:49:47: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:49:47: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:49:47: #1 total tags in treatment: 23193801 INFO @ Fri, 10 Dec 2021 12:49:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:49:47: #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 12:49:48: #1 tags after filtering in treatment: 23193692 INFO @ Fri, 10 Dec 2021 12:49:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:49:48: #1 finished! INFO @ Fri, 10 Dec 2021 12:49:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:49:50: #2 number of paired peaks: 204 WARNING @ Fri, 10 Dec 2021 12:49:50: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Fri, 10 Dec 2021 12:49:50: start model_add_line... INFO @ Fri, 10 Dec 2021 12:49:50: start X-correlation... INFO @ Fri, 10 Dec 2021 12:49:50: end of X-cor INFO @ Fri, 10 Dec 2021 12:49:50: #2 finished! INFO @ Fri, 10 Dec 2021 12:49:50: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 12:49:50: #2 alternative fragment length(s) may be 2,66 bps INFO @ Fri, 10 Dec 2021 12:49:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10_model.r WARNING @ Fri, 10 Dec 2021 12:49:50: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:49:50: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Fri, 10 Dec 2021 12:49:50: #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 12:49:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:49:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:49:50: 19000000 INFO @ Fri, 10 Dec 2021 12:49:56: 20000000 INFO @ Fri, 10 Dec 2021 12:49:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:50:01: 21000000 INFO @ Fri, 10 Dec 2021 12:50:07: 22000000 INFO @ Fri, 10 Dec 2021 12:50:13: 23000000 INFO @ Fri, 10 Dec 2021 12:50:14: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:50:14: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:50:14: #1 total tags in treatment: 23193801 INFO @ Fri, 10 Dec 2021 12:50:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:50:14: #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 12:50:14: #1 tags after filtering in treatment: 23193692 INFO @ Fri, 10 Dec 2021 12:50:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:50:14: #1 finished! INFO @ Fri, 10 Dec 2021 12:50:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05_summits.bed INFO @ Fri, 10 Dec 2021 12:50:15: Done! pass1 - making usageList (330 chroms): 2 millis pass2 - checking and writing primary data (1222 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:50:16: #2 number of paired peaks: 204 WARNING @ Fri, 10 Dec 2021 12:50:16: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Fri, 10 Dec 2021 12:50:16: start model_add_line... INFO @ Fri, 10 Dec 2021 12:50:16: start X-correlation... INFO @ Fri, 10 Dec 2021 12:50:16: end of X-cor INFO @ Fri, 10 Dec 2021 12:50:16: #2 finished! INFO @ Fri, 10 Dec 2021 12:50:16: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 12:50:16: #2 alternative fragment length(s) may be 2,66 bps INFO @ Fri, 10 Dec 2021 12:50:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20_model.r WARNING @ Fri, 10 Dec 2021 12:50:16: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:50:16: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Fri, 10 Dec 2021 12:50:16: #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 12:50:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:50:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:50:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:50:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:50:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:50:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10_summits.bed INFO @ Fri, 10 Dec 2021 12:50:47: Done! pass1 - making usageList (230 chroms): 0 millis pass2 - checking and writing primary data (648 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:50:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20_summits.bed INFO @ Fri, 10 Dec 2021 12:51:13: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 12 millis CompletedMACS2peakCalling