Job ID = 14170768 SRX = SRX8689000 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: 00:05:16 21040672 reads; of these: 21040672 (100.00%) were unpaired; of these: 633384 (3.01%) aligned 0 times 15297557 (72.70%) aligned exactly 1 time 5109731 (24.29%) aligned >1 times 96.99% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 2072234 / 20407288 = 0.1015 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 @ Sat, 11 Dec 2021 08:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.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 @ Sat, 11 Dec 2021 08:38:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:38:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:38:42: 1000000 INFO @ Sat, 11 Dec 2021 08:38:47: 2000000 INFO @ Sat, 11 Dec 2021 08:38:52: 3000000 INFO @ Sat, 11 Dec 2021 08:38:57: 4000000 INFO @ Sat, 11 Dec 2021 08:39:02: 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 @ Sat, 11 Dec 2021 08:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.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 @ Sat, 11 Dec 2021 08:39:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:39:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:39:07: 6000000 INFO @ Sat, 11 Dec 2021 08:39:12: 1000000 INFO @ Sat, 11 Dec 2021 08:39:13: 7000000 INFO @ Sat, 11 Dec 2021 08:39:17: 2000000 INFO @ Sat, 11 Dec 2021 08:39:18: 8000000 INFO @ Sat, 11 Dec 2021 08:39:23: 3000000 INFO @ Sat, 11 Dec 2021 08:39:24: 9000000 INFO @ Sat, 11 Dec 2021 08:39:28: 4000000 INFO @ Sat, 11 Dec 2021 08:39:29: 10000000 INFO @ Sat, 11 Dec 2021 08:39:33: 5000000 INFO @ Sat, 11 Dec 2021 08:39:34: 11000000 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 @ Sat, 11 Dec 2021 08:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.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 @ Sat, 11 Dec 2021 08:39:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:39:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:39:39: 6000000 INFO @ Sat, 11 Dec 2021 08:39:40: 12000000 INFO @ Sat, 11 Dec 2021 08:39:43: 1000000 INFO @ Sat, 11 Dec 2021 08:39:45: 7000000 INFO @ Sat, 11 Dec 2021 08:39:46: 13000000 INFO @ Sat, 11 Dec 2021 08:39:49: 2000000 INFO @ Sat, 11 Dec 2021 08:39:50: 8000000 INFO @ Sat, 11 Dec 2021 08:39:51: 14000000 INFO @ Sat, 11 Dec 2021 08:39:55: 3000000 INFO @ Sat, 11 Dec 2021 08:39:56: 9000000 INFO @ Sat, 11 Dec 2021 08:39:57: 15000000 INFO @ Sat, 11 Dec 2021 08:40:01: 4000000 INFO @ Sat, 11 Dec 2021 08:40:02: 10000000 INFO @ Sat, 11 Dec 2021 08:40:03: 16000000 INFO @ Sat, 11 Dec 2021 08:40:07: 11000000 INFO @ Sat, 11 Dec 2021 08:40:08: 5000000 INFO @ Sat, 11 Dec 2021 08:40:08: 17000000 INFO @ Sat, 11 Dec 2021 08:40:13: 12000000 INFO @ Sat, 11 Dec 2021 08:40:14: 6000000 INFO @ Sat, 11 Dec 2021 08:40:14: 18000000 INFO @ Sat, 11 Dec 2021 08:40:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:40:16: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:40:16: #1 total tags in treatment: 18335054 INFO @ Sat, 11 Dec 2021 08:40:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:40:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:40:17: #1 tags after filtering in treatment: 18335006 INFO @ Sat, 11 Dec 2021 08:40:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:40:17: #1 finished! INFO @ Sat, 11 Dec 2021 08:40:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:40:18: #2 number of paired peaks: 517 WARNING @ Sat, 11 Dec 2021 08:40:18: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 11 Dec 2021 08:40:18: start model_add_line... INFO @ Sat, 11 Dec 2021 08:40:18: start X-correlation... INFO @ Sat, 11 Dec 2021 08:40:18: end of X-cor INFO @ Sat, 11 Dec 2021 08:40:18: #2 finished! INFO @ Sat, 11 Dec 2021 08:40:18: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 08:40:18: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sat, 11 Dec 2021 08:40:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.05_model.r WARNING @ Sat, 11 Dec 2021 08:40:18: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:40:18: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sat, 11 Dec 2021 08:40:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:40:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:40:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:40:19: 13000000 INFO @ Sat, 11 Dec 2021 08:40:20: 7000000 INFO @ Sat, 11 Dec 2021 08:40:24: 14000000 INFO @ Sat, 11 Dec 2021 08:40:26: 8000000 INFO @ Sat, 11 Dec 2021 08:40:30: 15000000 INFO @ Sat, 11 Dec 2021 08:40:33: 9000000 INFO @ Sat, 11 Dec 2021 08:40:36: 16000000 INFO @ Sat, 11 Dec 2021 08:40:39: 10000000 INFO @ Sat, 11 Dec 2021 08:40:42: 17000000 INFO @ Sat, 11 Dec 2021 08:40:45: 11000000 INFO @ Sat, 11 Dec 2021 08:40:48: 18000000 INFO @ Sat, 11 Dec 2021 08:40:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:40:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:40:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:40:50: #1 total tags in treatment: 18335054 INFO @ Sat, 11 Dec 2021 08:40:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:40:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:40:50: #1 tags after filtering in treatment: 18335006 INFO @ Sat, 11 Dec 2021 08:40:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:40:50: #1 finished! INFO @ Sat, 11 Dec 2021 08:40:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:40:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:40:51: 12000000 INFO @ Sat, 11 Dec 2021 08:40:51: #2 number of paired peaks: 517 WARNING @ Sat, 11 Dec 2021 08:40:51: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 11 Dec 2021 08:40:51: start model_add_line... INFO @ Sat, 11 Dec 2021 08:40:51: start X-correlation... INFO @ Sat, 11 Dec 2021 08:40:51: end of X-cor INFO @ Sat, 11 Dec 2021 08:40:51: #2 finished! INFO @ Sat, 11 Dec 2021 08:40:51: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 08:40:51: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sat, 11 Dec 2021 08:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.10_model.r WARNING @ Sat, 11 Dec 2021 08:40:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:40:52: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sat, 11 Dec 2021 08:40:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:40:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:40:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:40:57: 13000000 INFO @ Sat, 11 Dec 2021 08:41:03: 14000000 INFO @ Sat, 11 Dec 2021 08:41:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:41:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:41:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.05_summits.bed INFO @ Sat, 11 Dec 2021 08:41:04: Done! pass1 - making usageList (689 chroms): 2 millis pass2 - checking and writing primary data (3286 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:41:09: 15000000 INFO @ Sat, 11 Dec 2021 08:41:15: 16000000 INFO @ Sat, 11 Dec 2021 08:41:21: 17000000 INFO @ Sat, 11 Dec 2021 08:41:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:41:27: 18000000 INFO @ Sat, 11 Dec 2021 08:41:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:41:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:41:29: #1 total tags in treatment: 18335054 INFO @ Sat, 11 Dec 2021 08:41:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:41:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:41:29: #1 tags after filtering in treatment: 18335006 INFO @ Sat, 11 Dec 2021 08:41:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:41:29: #1 finished! INFO @ Sat, 11 Dec 2021 08:41:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:41:30: #2 number of paired peaks: 517 WARNING @ Sat, 11 Dec 2021 08:41:30: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 11 Dec 2021 08:41:30: start model_add_line... INFO @ Sat, 11 Dec 2021 08:41:30: start X-correlation... INFO @ Sat, 11 Dec 2021 08:41:30: end of X-cor INFO @ Sat, 11 Dec 2021 08:41:30: #2 finished! INFO @ Sat, 11 Dec 2021 08:41:30: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 08:41:30: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sat, 11 Dec 2021 08:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.20_model.r WARNING @ Sat, 11 Dec 2021 08:41:30: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:41:30: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sat, 11 Dec 2021 08:41:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:41:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:41:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.10_summits.bed INFO @ Sat, 11 Dec 2021 08:41:37: Done! pass1 - making usageList (558 chroms): 2 millis pass2 - checking and writing primary data (2108 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:42:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:42:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:42:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:42:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689000/SRX8689000.20_summits.bed INFO @ Sat, 11 Dec 2021 08:42:16: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 10 millis CompletedMACS2peakCalling