Job ID = 14172820 SRX = SRX3293000 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: 00:13:57 29800365 reads; of these: 29800365 (100.00%) were unpaired; of these: 899079 (3.02%) aligned 0 times 24415371 (81.93%) aligned exactly 1 time 4485915 (15.05%) aligned >1 times 96.98% overall alignment rate Time searching: 00:13:57 Overall time: 00:13:57 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] 3119457 / 28901286 = 0.1079 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 17:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.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 17:27:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:27:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:27:08: 1000000 INFO @ Sat, 11 Dec 2021 17:27:15: 2000000 INFO @ Sat, 11 Dec 2021 17:27:23: 3000000 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 17:27:30: 4000000 INFO @ Sat, 11 Dec 2021 17:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.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 17:27:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:27:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:27:38: 5000000 INFO @ Sat, 11 Dec 2021 17:27:39: 1000000 INFO @ Sat, 11 Dec 2021 17:27:46: 6000000 INFO @ Sat, 11 Dec 2021 17:27:48: 2000000 INFO @ Sat, 11 Dec 2021 17:27:54: 7000000 INFO @ Sat, 11 Dec 2021 17:27:56: 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 17:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.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 17:28:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:28:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:28:03: 8000000 INFO @ Sat, 11 Dec 2021 17:28:05: 4000000 INFO @ Sat, 11 Dec 2021 17:28:11: 1000000 INFO @ Sat, 11 Dec 2021 17:28:12: 9000000 INFO @ Sat, 11 Dec 2021 17:28:15: 5000000 INFO @ Sat, 11 Dec 2021 17:28:21: 2000000 INFO @ Sat, 11 Dec 2021 17:28:22: 10000000 INFO @ Sat, 11 Dec 2021 17:28:24: 6000000 INFO @ Sat, 11 Dec 2021 17:28:31: 3000000 INFO @ Sat, 11 Dec 2021 17:28:32: 11000000 INFO @ Sat, 11 Dec 2021 17:28:34: 7000000 INFO @ Sat, 11 Dec 2021 17:28:41: 4000000 INFO @ Sat, 11 Dec 2021 17:28:42: 12000000 INFO @ Sat, 11 Dec 2021 17:28:44: 8000000 INFO @ Sat, 11 Dec 2021 17:28:51: 5000000 INFO @ Sat, 11 Dec 2021 17:28:52: 13000000 INFO @ Sat, 11 Dec 2021 17:28:54: 9000000 INFO @ Sat, 11 Dec 2021 17:29:01: 14000000 INFO @ Sat, 11 Dec 2021 17:29:01: 6000000 INFO @ Sat, 11 Dec 2021 17:29:04: 10000000 INFO @ Sat, 11 Dec 2021 17:29:11: 15000000 INFO @ Sat, 11 Dec 2021 17:29:12: 7000000 INFO @ Sat, 11 Dec 2021 17:29:13: 11000000 INFO @ Sat, 11 Dec 2021 17:29:21: 16000000 INFO @ Sat, 11 Dec 2021 17:29:24: 12000000 INFO @ Sat, 11 Dec 2021 17:29:25: 8000000 INFO @ Sat, 11 Dec 2021 17:29:31: 17000000 INFO @ Sat, 11 Dec 2021 17:29:34: 13000000 INFO @ Sat, 11 Dec 2021 17:29:38: 9000000 INFO @ Sat, 11 Dec 2021 17:29:41: 18000000 INFO @ Sat, 11 Dec 2021 17:29:43: 14000000 INFO @ Sat, 11 Dec 2021 17:29:48: 10000000 INFO @ Sat, 11 Dec 2021 17:29:50: 19000000 INFO @ Sat, 11 Dec 2021 17:29:53: 15000000 INFO @ Sat, 11 Dec 2021 17:29:58: 11000000 INFO @ Sat, 11 Dec 2021 17:30:00: 20000000 INFO @ Sat, 11 Dec 2021 17:30:03: 16000000 INFO @ Sat, 11 Dec 2021 17:30:08: 12000000 INFO @ Sat, 11 Dec 2021 17:30:10: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 17:30:12: 17000000 INFO @ Sat, 11 Dec 2021 17:30:18: 13000000 INFO @ Sat, 11 Dec 2021 17:30:20: 22000000 INFO @ Sat, 11 Dec 2021 17:30:22: 18000000 INFO @ Sat, 11 Dec 2021 17:30:28: 14000000 INFO @ Sat, 11 Dec 2021 17:30:29: 23000000 INFO @ Sat, 11 Dec 2021 17:30:31: 19000000 INFO @ Sat, 11 Dec 2021 17:30:38: 15000000 INFO @ Sat, 11 Dec 2021 17:30:39: 24000000 INFO @ Sat, 11 Dec 2021 17:30:41: 20000000 INFO @ Sat, 11 Dec 2021 17:30:47: 16000000 INFO @ Sat, 11 Dec 2021 17:30:48: 25000000 INFO @ Sat, 11 Dec 2021 17:30:51: 21000000 INFO @ Sat, 11 Dec 2021 17:30:56: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 17:30:56: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 17:30:56: #1 total tags in treatment: 25781829 INFO @ Sat, 11 Dec 2021 17:30:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:30:56: #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 17:30:57: #1 tags after filtering in treatment: 25781690 INFO @ Sat, 11 Dec 2021 17:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:30:57: #1 finished! INFO @ Sat, 11 Dec 2021 17:30:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:30:57: 17000000 INFO @ Sat, 11 Dec 2021 17:30:58: #2 number of paired peaks: 200 WARNING @ Sat, 11 Dec 2021 17:30:58: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 11 Dec 2021 17:30:58: start model_add_line... INFO @ Sat, 11 Dec 2021 17:30:58: start X-correlation... INFO @ Sat, 11 Dec 2021 17:30:58: end of X-cor INFO @ Sat, 11 Dec 2021 17:30:58: #2 finished! INFO @ Sat, 11 Dec 2021 17:30:58: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 17:30:58: #2 alternative fragment length(s) may be 1,94,569 bps INFO @ Sat, 11 Dec 2021 17:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.05_model.r WARNING @ Sat, 11 Dec 2021 17:30:58: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:30:58: #2 You may need to consider one of the other alternative d(s): 1,94,569 WARNING @ Sat, 11 Dec 2021 17:30:58: #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 17:30:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:31:00: 22000000 INFO @ Sat, 11 Dec 2021 17:31:07: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 17:31:09: 23000000 INFO @ Sat, 11 Dec 2021 17:31:17: 19000000 INFO @ Sat, 11 Dec 2021 17:31:19: 24000000 INFO @ Sat, 11 Dec 2021 17:31:27: 20000000 INFO @ Sat, 11 Dec 2021 17:31:28: 25000000 INFO @ Sat, 11 Dec 2021 17:31:35: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 17:31:35: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 17:31:35: #1 total tags in treatment: 25781829 INFO @ Sat, 11 Dec 2021 17:31:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:31:35: #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 17:31:36: #1 tags after filtering in treatment: 25781690 INFO @ Sat, 11 Dec 2021 17:31:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:31:36: #1 finished! INFO @ Sat, 11 Dec 2021 17:31:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:31:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:31:37: 21000000 INFO @ Sat, 11 Dec 2021 17:31:38: #2 number of paired peaks: 200 WARNING @ Sat, 11 Dec 2021 17:31:38: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 11 Dec 2021 17:31:38: start model_add_line... INFO @ Sat, 11 Dec 2021 17:31:38: start X-correlation... INFO @ Sat, 11 Dec 2021 17:31:38: end of X-cor INFO @ Sat, 11 Dec 2021 17:31:38: #2 finished! INFO @ Sat, 11 Dec 2021 17:31:38: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 17:31:38: #2 alternative fragment length(s) may be 1,94,569 bps INFO @ Sat, 11 Dec 2021 17:31:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.10_model.r WARNING @ Sat, 11 Dec 2021 17:31:38: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:31:38: #2 You may need to consider one of the other alternative d(s): 1,94,569 WARNING @ Sat, 11 Dec 2021 17:31:38: #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 17:31:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:31:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:31:45: 22000000 INFO @ Sat, 11 Dec 2021 17:31:54: 23000000 INFO @ Sat, 11 Dec 2021 17:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.05_peaks.xls INFO @ Sat, 11 Dec 2021 17:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.05_summits.bed INFO @ Sat, 11 Dec 2021 17:32:00: Done! pass1 - making usageList (409 chroms): 1 millis pass2 - checking and writing primary data (1198 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:32:03: 24000000 INFO @ Sat, 11 Dec 2021 17:32:12: 25000000 INFO @ Sat, 11 Dec 2021 17:32:19: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 17:32:19: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 17:32:19: #1 total tags in treatment: 25781829 INFO @ Sat, 11 Dec 2021 17:32:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:32:19: #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 17:32:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:32:20: #1 tags after filtering in treatment: 25781690 INFO @ Sat, 11 Dec 2021 17:32:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:32:20: #1 finished! INFO @ Sat, 11 Dec 2021 17:32:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:32:21: #2 number of paired peaks: 200 WARNING @ Sat, 11 Dec 2021 17:32:21: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 11 Dec 2021 17:32:21: start model_add_line... INFO @ Sat, 11 Dec 2021 17:32:21: start X-correlation... INFO @ Sat, 11 Dec 2021 17:32:21: end of X-cor INFO @ Sat, 11 Dec 2021 17:32:21: #2 finished! INFO @ Sat, 11 Dec 2021 17:32:21: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 17:32:21: #2 alternative fragment length(s) may be 1,94,569 bps INFO @ Sat, 11 Dec 2021 17:32:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.20_model.r WARNING @ Sat, 11 Dec 2021 17:32:21: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:32:21: #2 You may need to consider one of the other alternative d(s): 1,94,569 WARNING @ Sat, 11 Dec 2021 17:32:21: #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 17:32:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:32:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.10_peaks.xls INFO @ Sat, 11 Dec 2021 17:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.10_summits.bed INFO @ Sat, 11 Dec 2021 17:32:39: Done! pass1 - making usageList (328 chroms): 1 millis pass2 - checking and writing primary data (732 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:33:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.20_peaks.xls INFO @ Sat, 11 Dec 2021 17:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3293000/SRX3293000.20_summits.bed INFO @ Sat, 11 Dec 2021 17:33:23: Done! pass1 - making usageList (187 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 6 millis CompletedMACS2peakCalling