Job ID = 14170797 SRX = SRX8689008 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: 00:00:01 Multiseed full-index search: 00:10:48 23639722 reads; of these: 23639722 (100.00%) were unpaired; of these: 761153 (3.22%) aligned 0 times 15588758 (65.94%) aligned exactly 1 time 7289811 (30.84%) aligned >1 times 96.78% overall alignment rate Time searching: 00:10:49 Overall time: 00:10:49 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] 3454752 / 22878569 = 0.1510 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 09:03:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.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 09:03:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:03:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:03:19: 1000000 INFO @ Sat, 11 Dec 2021 09:03:29: 2000000 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 09:03:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.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 09:03:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:03:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:03:40: 3000000 INFO @ Sat, 11 Dec 2021 09:03:47: 1000000 INFO @ Sat, 11 Dec 2021 09:03:50: 4000000 INFO @ Sat, 11 Dec 2021 09:03:55: 2000000 INFO @ Sat, 11 Dec 2021 09:04:01: 5000000 INFO @ Sat, 11 Dec 2021 09:04:04: 3000000 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 09:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.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 09:04:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:04:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:04:12: 6000000 INFO @ Sat, 11 Dec 2021 09:04:12: 4000000 INFO @ Sat, 11 Dec 2021 09:04:18: 1000000 INFO @ Sat, 11 Dec 2021 09:04:21: 5000000 INFO @ Sat, 11 Dec 2021 09:04:23: 7000000 INFO @ Sat, 11 Dec 2021 09:04:28: 2000000 INFO @ Sat, 11 Dec 2021 09:04:30: 6000000 INFO @ Sat, 11 Dec 2021 09:04:34: 8000000 INFO @ Sat, 11 Dec 2021 09:04:38: 7000000 INFO @ Sat, 11 Dec 2021 09:04:38: 3000000 INFO @ Sat, 11 Dec 2021 09:04:45: 9000000 INFO @ Sat, 11 Dec 2021 09:04:47: 8000000 INFO @ Sat, 11 Dec 2021 09:04:48: 4000000 INFO @ Sat, 11 Dec 2021 09:04:55: 10000000 INFO @ Sat, 11 Dec 2021 09:04:56: 9000000 INFO @ Sat, 11 Dec 2021 09:04:58: 5000000 INFO @ Sat, 11 Dec 2021 09:05:04: 10000000 INFO @ Sat, 11 Dec 2021 09:05:06: 11000000 INFO @ Sat, 11 Dec 2021 09:05:07: 6000000 INFO @ Sat, 11 Dec 2021 09:05:13: 11000000 INFO @ Sat, 11 Dec 2021 09:05:17: 12000000 INFO @ Sat, 11 Dec 2021 09:05:17: 7000000 INFO @ Sat, 11 Dec 2021 09:05:22: 12000000 INFO @ Sat, 11 Dec 2021 09:05:27: 8000000 INFO @ Sat, 11 Dec 2021 09:05:28: 13000000 INFO @ Sat, 11 Dec 2021 09:05:31: 13000000 INFO @ Sat, 11 Dec 2021 09:05:37: 9000000 INFO @ Sat, 11 Dec 2021 09:05:38: 14000000 INFO @ Sat, 11 Dec 2021 09:05:39: 14000000 INFO @ Sat, 11 Dec 2021 09:05:47: 10000000 INFO @ Sat, 11 Dec 2021 09:05:49: 15000000 INFO @ Sat, 11 Dec 2021 09:05:49: 15000000 INFO @ Sat, 11 Dec 2021 09:05:57: 11000000 INFO @ Sat, 11 Dec 2021 09:05:58: 16000000 INFO @ Sat, 11 Dec 2021 09:06:00: 16000000 INFO @ Sat, 11 Dec 2021 09:06:07: 17000000 INFO @ Sat, 11 Dec 2021 09:06:07: 12000000 INFO @ Sat, 11 Dec 2021 09:06:11: 17000000 INFO @ Sat, 11 Dec 2021 09:06:16: 18000000 INFO @ Sat, 11 Dec 2021 09:06:17: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:06:22: 18000000 INFO @ Sat, 11 Dec 2021 09:06:26: 19000000 INFO @ Sat, 11 Dec 2021 09:06:27: 14000000 INFO @ Sat, 11 Dec 2021 09:06:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:06:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:06:30: #1 total tags in treatment: 19423817 INFO @ Sat, 11 Dec 2021 09:06:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:06:30: #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 09:06:31: #1 tags after filtering in treatment: 19423816 INFO @ Sat, 11 Dec 2021 09:06:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:06:31: #1 finished! INFO @ Sat, 11 Dec 2021 09:06:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:06:33: #2 number of paired peaks: 366 WARNING @ Sat, 11 Dec 2021 09:06:33: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Sat, 11 Dec 2021 09:06:33: start model_add_line... INFO @ Sat, 11 Dec 2021 09:06:33: start X-correlation... INFO @ Sat, 11 Dec 2021 09:06:33: end of X-cor INFO @ Sat, 11 Dec 2021 09:06:33: #2 finished! INFO @ Sat, 11 Dec 2021 09:06:33: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:06:33: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 11 Dec 2021 09:06:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.10_model.r WARNING @ Sat, 11 Dec 2021 09:06:33: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:06:33: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 11 Dec 2021 09:06:33: #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 09:06:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:06:33: 19000000 INFO @ Sat, 11 Dec 2021 09:06:37: 15000000 INFO @ Sat, 11 Dec 2021 09:06:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:06:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:06:38: #1 total tags in treatment: 19423817 INFO @ Sat, 11 Dec 2021 09:06:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:06:38: #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 09:06:39: #1 tags after filtering in treatment: 19423816 INFO @ Sat, 11 Dec 2021 09:06:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:06:39: #1 finished! INFO @ Sat, 11 Dec 2021 09:06:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:06:40: #2 number of paired peaks: 366 WARNING @ Sat, 11 Dec 2021 09:06:40: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Sat, 11 Dec 2021 09:06:40: start model_add_line... INFO @ Sat, 11 Dec 2021 09:06:41: start X-correlation... INFO @ Sat, 11 Dec 2021 09:06:41: end of X-cor INFO @ Sat, 11 Dec 2021 09:06:41: #2 finished! INFO @ Sat, 11 Dec 2021 09:06:41: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:06:41: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 11 Dec 2021 09:06:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.05_model.r WARNING @ Sat, 11 Dec 2021 09:06:41: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:06:41: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 11 Dec 2021 09:06:41: #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 09:06:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:06:47: 16000000 INFO @ Sat, 11 Dec 2021 09:06:57: 17000000 INFO @ Sat, 11 Dec 2021 09:07:07: 18000000 INFO @ Sat, 11 Dec 2021 09:07:17: 19000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:07:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:21: #1 total tags in treatment: 19423817 INFO @ Sat, 11 Dec 2021 09:07:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:21: #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 09:07:22: #1 tags after filtering in treatment: 19423816 INFO @ Sat, 11 Dec 2021 09:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:22: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:24: #2 number of paired peaks: 366 WARNING @ Sat, 11 Dec 2021 09:07:24: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:24: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:24: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:24: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:24: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:24: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 09:07:24: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 11 Dec 2021 09:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.20_model.r WARNING @ Sat, 11 Dec 2021 09:07:24: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:07:24: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 11 Dec 2021 09:07:24: #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 09:07:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:07:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.10_summits.bed INFO @ Sat, 11 Dec 2021 09:07:51: Done! pass1 - making usageList (570 chroms): 2 millis pass2 - checking and writing primary data (1830 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:07:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:07:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:07:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.05_summits.bed INFO @ Sat, 11 Dec 2021 09:07:54: Done! pass1 - making usageList (876 chroms): 2 millis pass2 - checking and writing primary data (4156 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:08:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689008/SRX8689008.20_summits.bed INFO @ Sat, 11 Dec 2021 09:08:42: Done! pass1 - making usageList (322 chroms): 3 millis pass2 - checking and writing primary data (714 records, 4 fields): 24 millis CompletedMACS2peakCalling