Job ID = 14172822 SRX = SRX7434111 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: 00:08:16 27316832 reads; of these: 27316832 (100.00%) were unpaired; of these: 3089530 (11.31%) aligned 0 times 18341119 (67.14%) aligned exactly 1 time 5886183 (21.55%) aligned >1 times 88.69% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 3732120 / 24227302 = 0.1540 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 17:18:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.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 17:18:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:18:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:18:38: 1000000 INFO @ Sat, 11 Dec 2021 17:18:49: 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 17:18:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.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 17:18:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:18:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:19:01: 3000000 INFO @ Sat, 11 Dec 2021 17:19:05: 1000000 INFO @ Sat, 11 Dec 2021 17:19:13: 4000000 INFO @ Sat, 11 Dec 2021 17:19:14: 2000000 INFO @ Sat, 11 Dec 2021 17:19:23: 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 17:19:26: 5000000 INFO @ Sat, 11 Dec 2021 17:19:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.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 17:19:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:19:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:19:33: 4000000 INFO @ Sat, 11 Dec 2021 17:19:36: 1000000 INFO @ Sat, 11 Dec 2021 17:19:38: 6000000 INFO @ Sat, 11 Dec 2021 17:19:43: 5000000 INFO @ Sat, 11 Dec 2021 17:19:46: 2000000 INFO @ Sat, 11 Dec 2021 17:19:50: 7000000 INFO @ Sat, 11 Dec 2021 17:19:52: 6000000 INFO @ Sat, 11 Dec 2021 17:19:55: 3000000 INFO @ Sat, 11 Dec 2021 17:20:02: 7000000 INFO @ Sat, 11 Dec 2021 17:20:02: 8000000 INFO @ Sat, 11 Dec 2021 17:20:05: 4000000 INFO @ Sat, 11 Dec 2021 17:20:12: 8000000 INFO @ Sat, 11 Dec 2021 17:20:14: 9000000 INFO @ Sat, 11 Dec 2021 17:20:15: 5000000 INFO @ Sat, 11 Dec 2021 17:20:21: 9000000 INFO @ Sat, 11 Dec 2021 17:20:25: 6000000 INFO @ Sat, 11 Dec 2021 17:20:26: 10000000 INFO @ Sat, 11 Dec 2021 17:20:31: 10000000 INFO @ Sat, 11 Dec 2021 17:20:34: 7000000 INFO @ Sat, 11 Dec 2021 17:20:38: 11000000 INFO @ Sat, 11 Dec 2021 17:20:40: 11000000 INFO @ Sat, 11 Dec 2021 17:20:44: 8000000 INFO @ Sat, 11 Dec 2021 17:20:50: 12000000 INFO @ Sat, 11 Dec 2021 17:20:50: 12000000 INFO @ Sat, 11 Dec 2021 17:20:54: 9000000 INFO @ Sat, 11 Dec 2021 17:21:00: 13000000 INFO @ Sat, 11 Dec 2021 17:21:02: 13000000 INFO @ Sat, 11 Dec 2021 17:21:04: 10000000 INFO @ Sat, 11 Dec 2021 17:21:10: 14000000 INFO @ Sat, 11 Dec 2021 17:21:14: 11000000 INFO @ Sat, 11 Dec 2021 17:21:14: 14000000 INFO @ Sat, 11 Dec 2021 17:21:20: 15000000 INFO @ Sat, 11 Dec 2021 17:21:23: 12000000 INFO @ Sat, 11 Dec 2021 17:21:27: 15000000 INFO @ Sat, 11 Dec 2021 17:21:29: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 17:21:33: 13000000 INFO @ Sat, 11 Dec 2021 17:21:39: 16000000 INFO @ Sat, 11 Dec 2021 17:21:40: 17000000 INFO @ Sat, 11 Dec 2021 17:21:43: 14000000 INFO @ Sat, 11 Dec 2021 17:21:50: 18000000 INFO @ Sat, 11 Dec 2021 17:21:52: 17000000 INFO @ Sat, 11 Dec 2021 17:21:53: 15000000 INFO @ Sat, 11 Dec 2021 17:21:59: 19000000 INFO @ Sat, 11 Dec 2021 17:22:03: 16000000 INFO @ Sat, 11 Dec 2021 17:22:04: 18000000 INFO @ Sat, 11 Dec 2021 17:22:10: 20000000 INFO @ Sat, 11 Dec 2021 17:22:14: 17000000 INFO @ Sat, 11 Dec 2021 17:22:15: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:22:15: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:22:15: #1 total tags in treatment: 20495182 INFO @ Sat, 11 Dec 2021 17:22:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:22:15: #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 17:22:16: #1 tags after filtering in treatment: 20495116 INFO @ Sat, 11 Dec 2021 17:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:22:16: #1 finished! INFO @ Sat, 11 Dec 2021 17:22:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:22:16: 19000000 INFO @ Sat, 11 Dec 2021 17:22:18: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 17:22:18: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 17:22:18: start model_add_line... INFO @ Sat, 11 Dec 2021 17:22:18: start X-correlation... INFO @ Sat, 11 Dec 2021 17:22:18: end of X-cor INFO @ Sat, 11 Dec 2021 17:22:18: #2 finished! INFO @ Sat, 11 Dec 2021 17:22:18: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 17:22:18: #2 alternative fragment length(s) may be 4,59,560 bps INFO @ Sat, 11 Dec 2021 17:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.10_model.r WARNING @ Sat, 11 Dec 2021 17:22:18: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:22:18: #2 You may need to consider one of the other alternative d(s): 4,59,560 WARNING @ Sat, 11 Dec 2021 17:22:18: #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 17:22:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:22:23: 18000000 INFO @ Sat, 11 Dec 2021 17:22:29: 20000000 INFO @ Sat, 11 Dec 2021 17:22:32: 19000000 INFO @ Sat, 11 Dec 2021 17:22:35: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:22:35: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:22:35: #1 total tags in treatment: 20495182 INFO @ Sat, 11 Dec 2021 17:22:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:22:35: #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 17:22:35: #1 tags after filtering in treatment: 20495116 INFO @ Sat, 11 Dec 2021 17:22:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:22:35: #1 finished! INFO @ Sat, 11 Dec 2021 17:22:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:22:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:22:37: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 17:22:37: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 17:22:37: start model_add_line... INFO @ Sat, 11 Dec 2021 17:22:37: start X-correlation... INFO @ Sat, 11 Dec 2021 17:22:37: end of X-cor INFO @ Sat, 11 Dec 2021 17:22:37: #2 finished! INFO @ Sat, 11 Dec 2021 17:22:37: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 17:22:37: #2 alternative fragment length(s) may be 4,59,560 bps INFO @ Sat, 11 Dec 2021 17:22:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.05_model.r WARNING @ Sat, 11 Dec 2021 17:22:37: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:22:37: #2 You may need to consider one of the other alternative d(s): 4,59,560 WARNING @ Sat, 11 Dec 2021 17:22:37: #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 17:22:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:22:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 17:22:41: 20000000 INFO @ Sat, 11 Dec 2021 17:22:46: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 17:22:46: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 17:22:46: #1 total tags in treatment: 20495182 INFO @ Sat, 11 Dec 2021 17:22:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:22:46: #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 17:22:47: #1 tags after filtering in treatment: 20495116 INFO @ Sat, 11 Dec 2021 17:22:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:22:47: #1 finished! INFO @ Sat, 11 Dec 2021 17:22:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:22:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:22:49: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 17:22:49: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 17:22:49: start model_add_line... INFO @ Sat, 11 Dec 2021 17:22:49: start X-correlation... INFO @ Sat, 11 Dec 2021 17:22:49: end of X-cor INFO @ Sat, 11 Dec 2021 17:22:49: #2 finished! INFO @ Sat, 11 Dec 2021 17:22:49: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 17:22:49: #2 alternative fragment length(s) may be 4,59,560 bps INFO @ Sat, 11 Dec 2021 17:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.20_model.r WARNING @ Sat, 11 Dec 2021 17:22:49: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:22:49: #2 You may need to consider one of the other alternative d(s): 4,59,560 WARNING @ Sat, 11 Dec 2021 17:22:49: #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 17:22:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:22:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:23:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:23:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.10_peaks.xls INFO @ Sat, 11 Dec 2021 17:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.10_summits.bed INFO @ Sat, 11 Dec 2021 17:23:36: Done! pass1 - making usageList (531 chroms): 2 millis pass2 - checking and writing primary data (1683 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:23:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.05_peaks.xls INFO @ Sat, 11 Dec 2021 17:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.05_summits.bed INFO @ Sat, 11 Dec 2021 17:23:55: Done! pass1 - making usageList (706 chroms): 3 millis pass2 - checking and writing primary data (4217 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.20_peaks.xls INFO @ Sat, 11 Dec 2021 17:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7434111/SRX7434111.20_summits.bed INFO @ Sat, 11 Dec 2021 17:24:07: Done! pass1 - making usageList (186 chroms): 2 millis pass2 - checking and writing primary data (359 records, 4 fields): 16 millis CompletedMACS2peakCalling