Job ID = 10166224 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:56:42: # 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 @ Thu, 08 Oct 2020 20:56:42: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:56:42: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:56:48: 1000000 INFO @ Thu, 08 Oct 2020 20:56:54: 2000000 INFO @ Thu, 08 Oct 2020 20:57:00: 3000000 INFO @ Thu, 08 Oct 2020 20:57:05: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:57:11: 5000000 INFO @ Thu, 08 Oct 2020 20:57:12: # 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 @ Thu, 08 Oct 2020 20:57:12: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:57:12: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:57:17: 6000000 INFO @ Thu, 08 Oct 2020 20:57:19: 1000000 INFO @ Thu, 08 Oct 2020 20:57:23: 7000000 INFO @ Thu, 08 Oct 2020 20:57:25: 2000000 INFO @ Thu, 08 Oct 2020 20:57:29: 8000000 INFO @ Thu, 08 Oct 2020 20:57:31: 3000000 INFO @ Thu, 08 Oct 2020 20:57:35: 9000000 INFO @ Thu, 08 Oct 2020 20:57:37: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:57:41: 10000000 INFO @ Thu, 08 Oct 2020 20:57:42: # 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 @ Thu, 08 Oct 2020 20:57:42: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:57:42: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:57:43: 5000000 INFO @ Thu, 08 Oct 2020 20:57:47: 11000000 INFO @ Thu, 08 Oct 2020 20:57:49: 1000000 INFO @ Thu, 08 Oct 2020 20:57:49: 6000000 INFO @ Thu, 08 Oct 2020 20:57:53: 12000000 INFO @ Thu, 08 Oct 2020 20:57:55: 2000000 INFO @ Thu, 08 Oct 2020 20:57:55: 7000000 INFO @ Thu, 08 Oct 2020 20:57:59: 13000000 INFO @ Thu, 08 Oct 2020 20:58:01: 3000000 INFO @ Thu, 08 Oct 2020 20:58:01: 8000000 INFO @ Thu, 08 Oct 2020 20:58:05: 14000000 INFO @ Thu, 08 Oct 2020 20:58:07: 4000000 INFO @ Thu, 08 Oct 2020 20:58:08: 9000000 INFO @ Thu, 08 Oct 2020 20:58:11: 15000000 INFO @ Thu, 08 Oct 2020 20:58:13: 5000000 INFO @ Thu, 08 Oct 2020 20:58:14: 10000000 INFO @ Thu, 08 Oct 2020 20:58:17: 16000000 INFO @ Thu, 08 Oct 2020 20:58:20: 6000000 INFO @ Thu, 08 Oct 2020 20:58:20: 11000000 INFO @ Thu, 08 Oct 2020 20:58:23: 17000000 INFO @ Thu, 08 Oct 2020 20:58:26: 7000000 INFO @ Thu, 08 Oct 2020 20:58:26: 12000000 INFO @ Thu, 08 Oct 2020 20:58:29: 18000000 INFO @ Thu, 08 Oct 2020 20:58:32: 8000000 INFO @ Thu, 08 Oct 2020 20:58:32: 13000000 INFO @ Thu, 08 Oct 2020 20:58:36: 19000000 INFO @ Thu, 08 Oct 2020 20:58:38: 9000000 INFO @ Thu, 08 Oct 2020 20:58:38: 14000000 INFO @ Thu, 08 Oct 2020 20:58:42: 20000000 INFO @ Thu, 08 Oct 2020 20:58:44: 10000000 INFO @ Thu, 08 Oct 2020 20:58:44: 15000000 INFO @ Thu, 08 Oct 2020 20:58:48: 21000000 INFO @ Thu, 08 Oct 2020 20:58:50: 11000000 INFO @ Thu, 08 Oct 2020 20:58:50: 16000000 INFO @ Thu, 08 Oct 2020 20:58:54: 22000000 INFO @ Thu, 08 Oct 2020 20:58:56: 12000000 INFO @ Thu, 08 Oct 2020 20:58:56: 17000000 INFO @ Thu, 08 Oct 2020 20:59:00: 23000000 INFO @ Thu, 08 Oct 2020 20:59:02: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:59:02: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:59:02: #1 total tags in treatment: 23193801 INFO @ Thu, 08 Oct 2020 20:59:02: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:59:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:59:02: 13000000 INFO @ Thu, 08 Oct 2020 20:59:02: #1 tags after filtering in treatment: 23193692 INFO @ Thu, 08 Oct 2020 20:59:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:59:02: #1 finished! INFO @ Thu, 08 Oct 2020 20:59:02: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:59:02: 18000000 INFO @ Thu, 08 Oct 2020 20:59:04: #2 number of paired peaks: 204 WARNING @ Thu, 08 Oct 2020 20:59:04: 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 @ Thu, 08 Oct 2020 20:59:04: start model_add_line... INFO @ Thu, 08 Oct 2020 20:59:04: start X-correlation... INFO @ Thu, 08 Oct 2020 20:59:04: end of X-cor INFO @ Thu, 08 Oct 2020 20:59:04: #2 finished! INFO @ Thu, 08 Oct 2020 20:59:04: #2 predicted fragment length is 66 bps INFO @ Thu, 08 Oct 2020 20:59:04: #2 alternative fragment length(s) may be 2,66 bps INFO @ Thu, 08 Oct 2020 20:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05_model.r WARNING @ Thu, 08 Oct 2020 20:59:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:59:04: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Thu, 08 Oct 2020 20:59:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:59:04: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:59:08: 14000000 INFO @ Thu, 08 Oct 2020 20:59:09: 19000000 INFO @ Thu, 08 Oct 2020 20:59:14: 15000000 INFO @ Thu, 08 Oct 2020 20:59:15: 20000000 INFO @ Thu, 08 Oct 2020 20:59:20: 16000000 INFO @ Thu, 08 Oct 2020 20:59:21: 21000000 INFO @ Thu, 08 Oct 2020 20:59:26: 17000000 INFO @ Thu, 08 Oct 2020 20:59:27: 22000000 INFO @ Thu, 08 Oct 2020 20:59:32: 18000000 INFO @ Thu, 08 Oct 2020 20:59:33: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:59:35: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:59:35: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:59:35: #1 total tags in treatment: 23193801 INFO @ Thu, 08 Oct 2020 20:59:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:59:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:59:35: #1 tags after filtering in treatment: 23193692 INFO @ Thu, 08 Oct 2020 20:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:59:35: #1 finished! INFO @ Thu, 08 Oct 2020 20:59:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:59:37: #2 number of paired peaks: 204 WARNING @ Thu, 08 Oct 2020 20:59:37: 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 @ Thu, 08 Oct 2020 20:59:37: start model_add_line... INFO @ Thu, 08 Oct 2020 20:59:37: start X-correlation... INFO @ Thu, 08 Oct 2020 20:59:37: end of X-cor INFO @ Thu, 08 Oct 2020 20:59:37: #2 finished! INFO @ Thu, 08 Oct 2020 20:59:37: #2 predicted fragment length is 66 bps INFO @ Thu, 08 Oct 2020 20:59:37: #2 alternative fragment length(s) may be 2,66 bps INFO @ Thu, 08 Oct 2020 20:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10_model.r WARNING @ Thu, 08 Oct 2020 20:59:37: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:59:37: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Thu, 08 Oct 2020 20:59:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:59:37: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:59:38: 19000000 INFO @ Thu, 08 Oct 2020 20:59:44: 20000000 INFO @ Thu, 08 Oct 2020 20:59:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:59:50: 21000000 INFO @ Thu, 08 Oct 2020 20:59:55: 22000000 INFO @ Thu, 08 Oct 2020 21:00:01: 23000000 INFO @ Thu, 08 Oct 2020 21:00:03: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:00:03: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:00:03: #1 total tags in treatment: 23193801 INFO @ Thu, 08 Oct 2020 21:00:03: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:00:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:00:03: #1 tags after filtering in treatment: 23193692 INFO @ Thu, 08 Oct 2020 21:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:00:03: #1 finished! INFO @ Thu, 08 Oct 2020 21:00:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:00:05: #2 number of paired peaks: 204 WARNING @ Thu, 08 Oct 2020 21:00:05: 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 @ Thu, 08 Oct 2020 21:00:05: start model_add_line... INFO @ Thu, 08 Oct 2020 21:00:05: start X-correlation... INFO @ Thu, 08 Oct 2020 21:00:05: end of X-cor INFO @ Thu, 08 Oct 2020 21:00:05: #2 finished! INFO @ Thu, 08 Oct 2020 21:00:05: #2 predicted fragment length is 66 bps INFO @ Thu, 08 Oct 2020 21:00:05: #2 alternative fragment length(s) may be 2,66 bps INFO @ Thu, 08 Oct 2020 21:00:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20_model.r WARNING @ Thu, 08 Oct 2020 21:00:05: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:00:05: #2 You may need to consider one of the other alternative d(s): 2,66 WARNING @ Thu, 08 Oct 2020 21:00:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:00:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:00:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:00:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:00:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:00:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.05_summits.bed INFO @ Thu, 08 Oct 2020 21:00:09: Done! pass1 - making usageList (330 chroms): 1 millis pass2 - checking and writing primary data (1222 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:00:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.10_summits.bed INFO @ Thu, 08 Oct 2020 21:00:42: Done! pass1 - making usageList (230 chroms): 1 millis pass2 - checking and writing primary data (648 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:00:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:01:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:01:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:01:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723697/SRX7723697.20_summits.bed INFO @ Thu, 08 Oct 2020 21:01:09: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 6 millis CompletedMACS2peakCalling