Job ID = 14170760 SRX = SRX8689103 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: 00:09:59 29136872 reads; of these: 29136872 (100.00%) were unpaired; of these: 928335 (3.19%) aligned 0 times 20483994 (70.30%) aligned exactly 1 time 7724543 (26.51%) aligned >1 times 96.81% overall alignment rate Time searching: 00:09:59 Overall time: 00:09:59 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] 4172243 / 28208537 = 0.1479 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 08:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.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 08:44:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:44:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:44:10: 1000000 INFO @ Sat, 11 Dec 2021 08:44:16: 2000000 INFO @ Sat, 11 Dec 2021 08:44:21: 3000000 INFO @ Sat, 11 Dec 2021 08:44:27: 4000000 INFO @ Sat, 11 Dec 2021 08:44:32: 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 08:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.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 08:44:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:44:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:44:38: 6000000 INFO @ Sat, 11 Dec 2021 08:44:40: 1000000 INFO @ Sat, 11 Dec 2021 08:44:43: 7000000 INFO @ Sat, 11 Dec 2021 08:44:46: 2000000 INFO @ Sat, 11 Dec 2021 08:44:49: 8000000 INFO @ Sat, 11 Dec 2021 08:44:51: 3000000 INFO @ Sat, 11 Dec 2021 08:44:54: 9000000 INFO @ Sat, 11 Dec 2021 08:44:57: 4000000 INFO @ Sat, 11 Dec 2021 08:45:00: 10000000 INFO @ Sat, 11 Dec 2021 08:45:02: 5000000 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 08:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.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 08:45:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:45:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:45:06: 11000000 INFO @ Sat, 11 Dec 2021 08:45:08: 6000000 INFO @ Sat, 11 Dec 2021 08:45:11: 1000000 INFO @ Sat, 11 Dec 2021 08:45:11: 12000000 INFO @ Sat, 11 Dec 2021 08:45:14: 7000000 INFO @ Sat, 11 Dec 2021 08:45:17: 13000000 INFO @ Sat, 11 Dec 2021 08:45:17: 2000000 INFO @ Sat, 11 Dec 2021 08:45:20: 8000000 INFO @ Sat, 11 Dec 2021 08:45:22: 14000000 INFO @ Sat, 11 Dec 2021 08:45:23: 3000000 INFO @ Sat, 11 Dec 2021 08:45:26: 9000000 INFO @ Sat, 11 Dec 2021 08:45:28: 15000000 INFO @ Sat, 11 Dec 2021 08:45:29: 4000000 INFO @ Sat, 11 Dec 2021 08:45:32: 10000000 INFO @ Sat, 11 Dec 2021 08:45:33: 16000000 INFO @ Sat, 11 Dec 2021 08:45:35: 5000000 INFO @ Sat, 11 Dec 2021 08:45:38: 11000000 INFO @ Sat, 11 Dec 2021 08:45:39: 17000000 INFO @ Sat, 11 Dec 2021 08:45:42: 6000000 INFO @ Sat, 11 Dec 2021 08:45:44: 12000000 INFO @ Sat, 11 Dec 2021 08:45:45: 18000000 INFO @ Sat, 11 Dec 2021 08:45:48: 7000000 INFO @ Sat, 11 Dec 2021 08:45:50: 13000000 INFO @ Sat, 11 Dec 2021 08:45:51: 19000000 INFO @ Sat, 11 Dec 2021 08:45:54: 8000000 INFO @ Sat, 11 Dec 2021 08:45:56: 14000000 INFO @ Sat, 11 Dec 2021 08:45:57: 20000000 INFO @ Sat, 11 Dec 2021 08:46:00: 9000000 INFO @ Sat, 11 Dec 2021 08:46:02: 15000000 INFO @ Sat, 11 Dec 2021 08:46:02: 21000000 INFO @ Sat, 11 Dec 2021 08:46:05: 10000000 INFO @ Sat, 11 Dec 2021 08:46:08: 22000000 INFO @ Sat, 11 Dec 2021 08:46:11: 16000000 INFO @ Sat, 11 Dec 2021 08:46:11: 11000000 INFO @ Sat, 11 Dec 2021 08:46:15: 23000000 INFO @ Sat, 11 Dec 2021 08:46:16: 12000000 INFO @ Sat, 11 Dec 2021 08:46:18: 17000000 INFO @ Sat, 11 Dec 2021 08:46:22: 24000000 INFO @ Sat, 11 Dec 2021 08:46:22: 13000000 INFO @ Sat, 11 Dec 2021 08:46:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:46:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:46:22: #1 total tags in treatment: 24036294 INFO @ Sat, 11 Dec 2021 08:46:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:46:22: #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 08:46:23: #1 tags after filtering in treatment: 24036241 INFO @ Sat, 11 Dec 2021 08:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:46:23: #1 finished! INFO @ Sat, 11 Dec 2021 08:46:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:46:25: #2 number of paired peaks: 445 WARNING @ Sat, 11 Dec 2021 08:46:25: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sat, 11 Dec 2021 08:46:25: start model_add_line... INFO @ Sat, 11 Dec 2021 08:46:26: start X-correlation... INFO @ Sat, 11 Dec 2021 08:46:26: end of X-cor INFO @ Sat, 11 Dec 2021 08:46:26: #2 finished! INFO @ Sat, 11 Dec 2021 08:46:26: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 08:46:26: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 11 Dec 2021 08:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.05_model.r WARNING @ Sat, 11 Dec 2021 08:46:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:46:26: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 11 Dec 2021 08:46:26: #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 08:46:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:46:26: 18000000 INFO @ Sat, 11 Dec 2021 08:46:29: 14000000 INFO @ Sat, 11 Dec 2021 08:46:34: 19000000 INFO @ Sat, 11 Dec 2021 08:46:36: 15000000 INFO @ Sat, 11 Dec 2021 08:46:41: 20000000 INFO @ Sat, 11 Dec 2021 08:46:41: 16000000 INFO @ Sat, 11 Dec 2021 08:46:46: 17000000 INFO @ Sat, 11 Dec 2021 08:46:47: 21000000 INFO @ Sat, 11 Dec 2021 08:46:52: 18000000 INFO @ Sat, 11 Dec 2021 08:46:53: 22000000 INFO @ Sat, 11 Dec 2021 08:46:58: 23000000 INFO @ Sat, 11 Dec 2021 08:46:59: 19000000 INFO @ Sat, 11 Dec 2021 08:47:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:47:05: 20000000 INFO @ Sat, 11 Dec 2021 08:47:05: 24000000 INFO @ Sat, 11 Dec 2021 08:47:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:47:05: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:47:05: #1 total tags in treatment: 24036294 INFO @ Sat, 11 Dec 2021 08:47:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:47:05: #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 08:47:06: #1 tags after filtering in treatment: 24036241 INFO @ Sat, 11 Dec 2021 08:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:47:06: #1 finished! INFO @ Sat, 11 Dec 2021 08:47:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:47:08: #2 number of paired peaks: 445 WARNING @ Sat, 11 Dec 2021 08:47:08: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sat, 11 Dec 2021 08:47:08: start model_add_line... INFO @ Sat, 11 Dec 2021 08:47:08: start X-correlation... INFO @ Sat, 11 Dec 2021 08:47:08: end of X-cor INFO @ Sat, 11 Dec 2021 08:47:08: #2 finished! INFO @ Sat, 11 Dec 2021 08:47:08: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 08:47:08: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 11 Dec 2021 08:47:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.10_model.r WARNING @ Sat, 11 Dec 2021 08:47:08: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:47:08: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 11 Dec 2021 08:47:08: #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 08:47:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:47:10: 21000000 INFO @ Sat, 11 Dec 2021 08:47:15: 22000000 INFO @ Sat, 11 Dec 2021 08:47:21: 23000000 INFO @ Sat, 11 Dec 2021 08:47:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:47:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:47:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.05_summits.bed INFO @ Sat, 11 Dec 2021 08:47:24: Done! pass1 - making usageList (716 chroms): 2 millis pass2 - checking and writing primary data (3598 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:47:26: 24000000 INFO @ Sat, 11 Dec 2021 08:47:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:47:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:47:27: #1 total tags in treatment: 24036294 INFO @ Sat, 11 Dec 2021 08:47:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:47:27: #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 08:47:28: #1 tags after filtering in treatment: 24036241 INFO @ Sat, 11 Dec 2021 08:47:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:47:28: #1 finished! INFO @ Sat, 11 Dec 2021 08:47:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:47:29: #2 number of paired peaks: 445 WARNING @ Sat, 11 Dec 2021 08:47:29: Fewer paired peaks (445) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 445 pairs to build model! INFO @ Sat, 11 Dec 2021 08:47:29: start model_add_line... INFO @ Sat, 11 Dec 2021 08:47:29: start X-correlation... INFO @ Sat, 11 Dec 2021 08:47:29: end of X-cor INFO @ Sat, 11 Dec 2021 08:47:29: #2 finished! INFO @ Sat, 11 Dec 2021 08:47:29: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 08:47:29: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sat, 11 Dec 2021 08:47:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.20_model.r WARNING @ Sat, 11 Dec 2021 08:47:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:47:30: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sat, 11 Dec 2021 08:47:30: #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 08:47:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:47:30: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:47:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.10_summits.bed INFO @ Sat, 11 Dec 2021 08:48:06: Done! pass1 - making usageList (620 chroms): 2 millis pass2 - checking and writing primary data (2527 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:48:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:48:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:48:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:48:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689103/SRX8689103.20_summits.bed INFO @ Sat, 11 Dec 2021 08:48:28: Done! pass1 - making usageList (418 chroms): 1 millis pass2 - checking and writing primary data (1073 records, 4 fields): 27 millis CompletedMACS2peakCalling BigWig に変換しました。