Job ID = 14171487 SRX = SRX10971120 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:48:32 prefetch.2.10.7: 1) Downloading 'SRR14631244'... 2021-12-11T02:48:32 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:50:13 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:50:13 prefetch.2.10.7: 1) 'SRR14631244' was downloaded successfully 2021-12-11T02:50:13 prefetch.2.10.7: 'SRR14631244' has 0 unresolved dependencies Read 24963861 spots for SRR14631244/SRR14631244.sra Written 24963861 spots for SRR14631244/SRR14631244.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172327 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:28:41 24963861 reads; of these: 24963861 (100.00%) were paired; of these: 2569352 (10.29%) aligned concordantly 0 times 16843428 (67.47%) aligned concordantly exactly 1 time 5551081 (22.24%) aligned concordantly >1 times ---- 2569352 pairs aligned concordantly 0 times; of these: 309517 (12.05%) aligned discordantly 1 time ---- 2259835 pairs aligned 0 times concordantly or discordantly; of these: 4519670 mates make up the pairs; of these: 3123059 (69.10%) aligned 0 times 499857 (11.06%) aligned exactly 1 time 896754 (19.84%) aligned >1 times 93.74% overall alignment rate Time searching: 01:28:41 Overall time: 01:28:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 12120112 / 22584826 = 0.5366 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 13:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.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 13:32:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:32:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:32:17: 1000000 INFO @ Sat, 11 Dec 2021 13:32:22: 2000000 INFO @ Sat, 11 Dec 2021 13:32:27: 3000000 INFO @ Sat, 11 Dec 2021 13:32:33: 4000000 INFO @ Sat, 11 Dec 2021 13:32:38: 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 13:32:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.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 13:32:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:32:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:32:44: 6000000 INFO @ Sat, 11 Dec 2021 13:32:47: 1000000 INFO @ Sat, 11 Dec 2021 13:32:50: 7000000 INFO @ Sat, 11 Dec 2021 13:32:53: 2000000 INFO @ Sat, 11 Dec 2021 13:32:57: 8000000 INFO @ Sat, 11 Dec 2021 13:32:59: 3000000 INFO @ Sat, 11 Dec 2021 13:33:03: 9000000 INFO @ Sat, 11 Dec 2021 13:33:05: 4000000 INFO @ Sat, 11 Dec 2021 13:33:09: 10000000 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 13:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.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 13:33:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:33:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:33:12: 5000000 INFO @ Sat, 11 Dec 2021 13:33:15: 11000000 INFO @ Sat, 11 Dec 2021 13:33:17: 1000000 INFO @ Sat, 11 Dec 2021 13:33:18: 6000000 INFO @ Sat, 11 Dec 2021 13:33:21: 12000000 INFO @ Sat, 11 Dec 2021 13:33:23: 2000000 INFO @ Sat, 11 Dec 2021 13:33:24: 7000000 INFO @ Sat, 11 Dec 2021 13:33:27: 13000000 INFO @ Sat, 11 Dec 2021 13:33:30: 3000000 INFO @ Sat, 11 Dec 2021 13:33:30: 8000000 INFO @ Sat, 11 Dec 2021 13:33:33: 14000000 INFO @ Sat, 11 Dec 2021 13:33:36: 4000000 INFO @ Sat, 11 Dec 2021 13:33:37: 9000000 INFO @ Sat, 11 Dec 2021 13:33:39: 15000000 INFO @ Sat, 11 Dec 2021 13:33:42: 5000000 INFO @ Sat, 11 Dec 2021 13:33:43: 10000000 INFO @ Sat, 11 Dec 2021 13:33:45: 16000000 INFO @ Sat, 11 Dec 2021 13:33:49: 6000000 INFO @ Sat, 11 Dec 2021 13:33:49: 11000000 INFO @ Sat, 11 Dec 2021 13:33:52: 17000000 INFO @ Sat, 11 Dec 2021 13:33:55: 7000000 INFO @ Sat, 11 Dec 2021 13:33:55: 12000000 INFO @ Sat, 11 Dec 2021 13:33:58: 18000000 INFO @ Sat, 11 Dec 2021 13:34:01: 8000000 INFO @ Sat, 11 Dec 2021 13:34:01: 13000000 INFO @ Sat, 11 Dec 2021 13:34:04: 19000000 INFO @ Sat, 11 Dec 2021 13:34:07: 9000000 INFO @ Sat, 11 Dec 2021 13:34:08: 14000000 INFO @ Sat, 11 Dec 2021 13:34:10: 20000000 INFO @ Sat, 11 Dec 2021 13:34:14: 10000000 INFO @ Sat, 11 Dec 2021 13:34:14: 15000000 INFO @ Sat, 11 Dec 2021 13:34:17: 21000000 INFO @ Sat, 11 Dec 2021 13:34:20: 11000000 INFO @ Sat, 11 Dec 2021 13:34:20: 16000000 INFO @ Sat, 11 Dec 2021 13:34:23: 22000000 INFO @ Sat, 11 Dec 2021 13:34:26: 12000000 INFO @ Sat, 11 Dec 2021 13:34:26: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:34:26: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:34:26: #1 total tags in treatment: 10373842 INFO @ Sat, 11 Dec 2021 13:34:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:34:26: #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 13:34:26: #1 tags after filtering in treatment: 9809123 INFO @ Sat, 11 Dec 2021 13:34:26: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:34:26: #1 finished! INFO @ Sat, 11 Dec 2021 13:34:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:34:26: 17000000 INFO @ Sat, 11 Dec 2021 13:34:27: #2 number of paired peaks: 298 WARNING @ Sat, 11 Dec 2021 13:34:27: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 11 Dec 2021 13:34:27: start model_add_line... INFO @ Sat, 11 Dec 2021 13:34:27: start X-correlation... INFO @ Sat, 11 Dec 2021 13:34:27: end of X-cor INFO @ Sat, 11 Dec 2021 13:34:27: #2 finished! INFO @ Sat, 11 Dec 2021 13:34:27: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 13:34:27: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 11 Dec 2021 13:34:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.05_model.r WARNING @ Sat, 11 Dec 2021 13:34:27: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:34:27: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Sat, 11 Dec 2021 13:34:27: #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 13:34:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:34:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:34:32: 13000000 INFO @ Sat, 11 Dec 2021 13:34:33: 18000000 INFO @ Sat, 11 Dec 2021 13:34:38: 14000000 INFO @ Sat, 11 Dec 2021 13:34:39: 19000000 INFO @ Sat, 11 Dec 2021 13:34:44: 15000000 INFO @ Sat, 11 Dec 2021 13:34:46: 20000000 INFO @ Sat, 11 Dec 2021 13:34:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:34:51: 16000000 INFO @ Sat, 11 Dec 2021 13:34:52: 21000000 INFO @ Sat, 11 Dec 2021 13:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.05_summits.bed INFO @ Sat, 11 Dec 2021 13:34:56: Done! INFO @ Sat, 11 Dec 2021 13:34:57: 17000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3850 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:34:58: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:35:02: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:35:02: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:35:02: #1 total tags in treatment: 10373842 INFO @ Sat, 11 Dec 2021 13:35:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:35:02: #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 13:35:02: #1 tags after filtering in treatment: 9809123 INFO @ Sat, 11 Dec 2021 13:35:02: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:35:02: #1 finished! INFO @ Sat, 11 Dec 2021 13:35:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:35:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:35:03: #2 number of paired peaks: 298 WARNING @ Sat, 11 Dec 2021 13:35:03: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 11 Dec 2021 13:35:03: start model_add_line... INFO @ Sat, 11 Dec 2021 13:35:03: start X-correlation... INFO @ Sat, 11 Dec 2021 13:35:03: end of X-cor INFO @ Sat, 11 Dec 2021 13:35:03: #2 finished! INFO @ Sat, 11 Dec 2021 13:35:03: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 13:35:03: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 11 Dec 2021 13:35:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.10_model.r WARNING @ Sat, 11 Dec 2021 13:35:03: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:35:03: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Sat, 11 Dec 2021 13:35:03: #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 13:35:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:35:03: 18000000 INFO @ Sat, 11 Dec 2021 13:35:09: 19000000 INFO @ Sat, 11 Dec 2021 13:35:16: 20000000 INFO @ Sat, 11 Dec 2021 13:35:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:35:22: 21000000 INFO @ Sat, 11 Dec 2021 13:35:28: 22000000 INFO @ Sat, 11 Dec 2021 13:35:31: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:35:31: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:35:31: #1 total tags in treatment: 10373842 INFO @ Sat, 11 Dec 2021 13:35:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:35:31: #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 13:35:31: #1 tags after filtering in treatment: 9809123 INFO @ Sat, 11 Dec 2021 13:35:31: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:35:31: #1 finished! INFO @ Sat, 11 Dec 2021 13:35:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:35:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:35:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:35:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.10_summits.bed INFO @ Sat, 11 Dec 2021 13:35:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1616 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:35:32: #2 number of paired peaks: 298 WARNING @ Sat, 11 Dec 2021 13:35:32: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sat, 11 Dec 2021 13:35:32: start model_add_line... INFO @ Sat, 11 Dec 2021 13:35:32: start X-correlation... INFO @ Sat, 11 Dec 2021 13:35:32: end of X-cor INFO @ Sat, 11 Dec 2021 13:35:32: #2 finished! INFO @ Sat, 11 Dec 2021 13:35:32: #2 predicted fragment length is 158 bps INFO @ Sat, 11 Dec 2021 13:35:32: #2 alternative fragment length(s) may be 158 bps INFO @ Sat, 11 Dec 2021 13:35:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.20_model.r WARNING @ Sat, 11 Dec 2021 13:35:32: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:35:32: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Sat, 11 Dec 2021 13:35:32: #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 13:35:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:35:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:35:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:36:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:36:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:36:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971120/SRX10971120.20_summits.bed INFO @ Sat, 11 Dec 2021 13:36:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 2 millis CompletedMACS2peakCalling