Job ID = 12265556 SRX = SRX7277021 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36172501 spots for SRR10597286/SRR10597286.sra Written 36172501 spots for SRR10597286/SRR10597286.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265930 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:48:47 36172501 reads; of these: 36172501 (100.00%) were paired; of these: 13279539 (36.71%) aligned concordantly 0 times 11675304 (32.28%) aligned concordantly exactly 1 time 11217658 (31.01%) aligned concordantly >1 times ---- 13279539 pairs aligned concordantly 0 times; of these: 2535621 (19.09%) aligned discordantly 1 time ---- 10743918 pairs aligned 0 times concordantly or discordantly; of these: 21487836 mates make up the pairs; of these: 15882104 (73.91%) aligned 0 times 844520 (3.93%) aligned exactly 1 time 4761212 (22.16%) aligned >1 times 78.05% overall alignment rate Time searching: 00:48:48 Overall time: 00:48:48 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 24 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] 9253059 / 25211133 = 0.3670 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.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, 03 Apr 2021 08:42:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:42:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:42:50: 1000000 INFO @ Sat, 03 Apr 2021 08:42:57: 2000000 INFO @ Sat, 03 Apr 2021 08:43:04: 3000000 INFO @ Sat, 03 Apr 2021 08:43:10: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:43:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.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, 03 Apr 2021 08:43:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:43:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:43:17: 5000000 INFO @ Sat, 03 Apr 2021 08:43:20: 1000000 INFO @ Sat, 03 Apr 2021 08:43:25: 6000000 INFO @ Sat, 03 Apr 2021 08:43:28: 2000000 INFO @ Sat, 03 Apr 2021 08:43:32: 7000000 INFO @ Sat, 03 Apr 2021 08:43:36: 3000000 INFO @ Sat, 03 Apr 2021 08:43:39: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:43:43: 4000000 INFO @ Sat, 03 Apr 2021 08:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.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, 03 Apr 2021 08:43:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:43:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:43:46: 9000000 INFO @ Sat, 03 Apr 2021 08:43:51: 5000000 INFO @ Sat, 03 Apr 2021 08:43:51: 1000000 INFO @ Sat, 03 Apr 2021 08:43:54: 10000000 INFO @ Sat, 03 Apr 2021 08:43:58: 6000000 INFO @ Sat, 03 Apr 2021 08:43:58: 2000000 INFO @ Sat, 03 Apr 2021 08:44:02: 11000000 INFO @ Sat, 03 Apr 2021 08:44:06: 3000000 INFO @ Sat, 03 Apr 2021 08:44:06: 7000000 INFO @ Sat, 03 Apr 2021 08:44:09: 12000000 INFO @ Sat, 03 Apr 2021 08:44:13: 8000000 INFO @ Sat, 03 Apr 2021 08:44:13: 4000000 INFO @ Sat, 03 Apr 2021 08:44:17: 13000000 INFO @ Sat, 03 Apr 2021 08:44:20: 5000000 INFO @ Sat, 03 Apr 2021 08:44:21: 9000000 INFO @ Sat, 03 Apr 2021 08:44:25: 14000000 INFO @ Sat, 03 Apr 2021 08:44:28: 6000000 INFO @ Sat, 03 Apr 2021 08:44:29: 10000000 INFO @ Sat, 03 Apr 2021 08:44:33: 15000000 INFO @ Sat, 03 Apr 2021 08:44:35: 7000000 INFO @ Sat, 03 Apr 2021 08:44:36: 11000000 INFO @ Sat, 03 Apr 2021 08:44:40: 16000000 INFO @ Sat, 03 Apr 2021 08:44:43: 8000000 INFO @ Sat, 03 Apr 2021 08:44:44: 12000000 INFO @ Sat, 03 Apr 2021 08:44:48: 17000000 INFO @ Sat, 03 Apr 2021 08:44:51: 9000000 INFO @ Sat, 03 Apr 2021 08:44:52: 13000000 INFO @ Sat, 03 Apr 2021 08:44:56: 18000000 INFO @ Sat, 03 Apr 2021 08:44:58: 10000000 INFO @ Sat, 03 Apr 2021 08:45:00: 14000000 INFO @ Sat, 03 Apr 2021 08:45:03: 19000000 INFO @ Sat, 03 Apr 2021 08:45:06: 11000000 INFO @ Sat, 03 Apr 2021 08:45:08: 15000000 INFO @ Sat, 03 Apr 2021 08:45:11: 20000000 INFO @ Sat, 03 Apr 2021 08:45:14: 12000000 INFO @ Sat, 03 Apr 2021 08:45:15: 16000000 INFO @ Sat, 03 Apr 2021 08:45:19: 21000000 INFO @ Sat, 03 Apr 2021 08:45:21: 13000000 INFO @ Sat, 03 Apr 2021 08:45:23: 17000000 INFO @ Sat, 03 Apr 2021 08:45:26: 22000000 INFO @ Sat, 03 Apr 2021 08:45:29: 14000000 INFO @ Sat, 03 Apr 2021 08:45:31: 18000000 INFO @ Sat, 03 Apr 2021 08:45:33: 23000000 INFO @ Sat, 03 Apr 2021 08:45:37: 15000000 INFO @ Sat, 03 Apr 2021 08:45:38: 19000000 INFO @ Sat, 03 Apr 2021 08:45:41: 24000000 INFO @ Sat, 03 Apr 2021 08:45:45: 16000000 INFO @ Sat, 03 Apr 2021 08:45:46: 20000000 INFO @ Sat, 03 Apr 2021 08:45:48: 25000000 INFO @ Sat, 03 Apr 2021 08:45:53: 17000000 INFO @ Sat, 03 Apr 2021 08:45:54: 21000000 INFO @ Sat, 03 Apr 2021 08:45:56: 26000000 INFO @ Sat, 03 Apr 2021 08:46:00: 18000000 INFO @ Sat, 03 Apr 2021 08:46:02: 22000000 INFO @ Sat, 03 Apr 2021 08:46:04: 27000000 INFO @ Sat, 03 Apr 2021 08:46:08: 19000000 INFO @ Sat, 03 Apr 2021 08:46:09: 23000000 INFO @ Sat, 03 Apr 2021 08:46:11: 28000000 INFO @ Sat, 03 Apr 2021 08:46:16: 20000000 INFO @ Sat, 03 Apr 2021 08:46:17: 24000000 INFO @ Sat, 03 Apr 2021 08:46:19: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:46:24: 21000000 INFO @ Sat, 03 Apr 2021 08:46:24: 25000000 INFO @ Sat, 03 Apr 2021 08:46:27: 30000000 INFO @ Sat, 03 Apr 2021 08:46:31: 22000000 INFO @ Sat, 03 Apr 2021 08:46:32: 26000000 INFO @ Sat, 03 Apr 2021 08:46:35: 31000000 INFO @ Sat, 03 Apr 2021 08:46:39: 23000000 INFO @ Sat, 03 Apr 2021 08:46:39: 27000000 INFO @ Sat, 03 Apr 2021 08:46:43: 32000000 INFO @ Sat, 03 Apr 2021 08:46:47: 28000000 INFO @ Sat, 03 Apr 2021 08:46:47: 24000000 INFO @ Sat, 03 Apr 2021 08:46:51: 33000000 INFO @ Sat, 03 Apr 2021 08:46:54: 29000000 INFO @ Sat, 03 Apr 2021 08:46:55: 25000000 INFO @ Sat, 03 Apr 2021 08:46:59: 34000000 INFO @ Sat, 03 Apr 2021 08:47:02: 30000000 INFO @ Sat, 03 Apr 2021 08:47:02: 26000000 INFO @ Sat, 03 Apr 2021 08:47:07: 35000000 INFO @ Sat, 03 Apr 2021 08:47:10: 31000000 INFO @ Sat, 03 Apr 2021 08:47:10: 27000000 INFO @ Sat, 03 Apr 2021 08:47:15: 36000000 INFO @ Sat, 03 Apr 2021 08:47:18: 32000000 INFO @ Sat, 03 Apr 2021 08:47:18: 28000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:47:23: 37000000 INFO @ Sat, 03 Apr 2021 08:47:26: 33000000 INFO @ Sat, 03 Apr 2021 08:47:26: 29000000 INFO @ Sat, 03 Apr 2021 08:47:31: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:47:31: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:47:31: #1 total tags in treatment: 13965934 INFO @ Sat, 03 Apr 2021 08:47:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:47:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:47:31: #1 tags after filtering in treatment: 10719397 INFO @ Sat, 03 Apr 2021 08:47:31: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 08:47:31: #1 finished! INFO @ Sat, 03 Apr 2021 08:47:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:47:32: #2 number of paired peaks: 246 WARNING @ Sat, 03 Apr 2021 08:47:32: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 03 Apr 2021 08:47:32: start model_add_line... INFO @ Sat, 03 Apr 2021 08:47:32: start X-correlation... INFO @ Sat, 03 Apr 2021 08:47:32: end of X-cor INFO @ Sat, 03 Apr 2021 08:47:32: #2 finished! INFO @ Sat, 03 Apr 2021 08:47:32: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 08:47:32: #2 alternative fragment length(s) may be 4,107,581 bps INFO @ Sat, 03 Apr 2021 08:47:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.05_model.r WARNING @ Sat, 03 Apr 2021 08:47:32: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:47:32: #2 You may need to consider one of the other alternative d(s): 4,107,581 WARNING @ Sat, 03 Apr 2021 08:47:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:47:32: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:47:33: 34000000 INFO @ Sat, 03 Apr 2021 08:47:34: 30000000 INFO @ Sat, 03 Apr 2021 08:47:41: 31000000 INFO @ Sat, 03 Apr 2021 08:47:41: 35000000 INFO @ Sat, 03 Apr 2021 08:47:48: 32000000 INFO @ Sat, 03 Apr 2021 08:47:49: 36000000 INFO @ Sat, 03 Apr 2021 08:47:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:47:56: 33000000 INFO @ Sat, 03 Apr 2021 08:47:57: 37000000 INFO @ Sat, 03 Apr 2021 08:48:03: 34000000 INFO @ Sat, 03 Apr 2021 08:48:04: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:48:04: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:48:04: #1 total tags in treatment: 13965934 INFO @ Sat, 03 Apr 2021 08:48:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:48:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:48:04: #1 tags after filtering in treatment: 10719397 INFO @ Sat, 03 Apr 2021 08:48:04: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 08:48:04: #1 finished! INFO @ Sat, 03 Apr 2021 08:48:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:48:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:48:05: #2 number of paired peaks: 246 WARNING @ Sat, 03 Apr 2021 08:48:05: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 03 Apr 2021 08:48:05: start model_add_line... INFO @ Sat, 03 Apr 2021 08:48:05: start X-correlation... INFO @ Sat, 03 Apr 2021 08:48:05: end of X-cor INFO @ Sat, 03 Apr 2021 08:48:05: #2 finished! INFO @ Sat, 03 Apr 2021 08:48:05: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 08:48:05: #2 alternative fragment length(s) may be 4,107,581 bps INFO @ Sat, 03 Apr 2021 08:48:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.10_model.r WARNING @ Sat, 03 Apr 2021 08:48:05: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:48:05: #2 You may need to consider one of the other alternative d(s): 4,107,581 WARNING @ Sat, 03 Apr 2021 08:48:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:48:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:48:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.05_summits.bed INFO @ Sat, 03 Apr 2021 08:48:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4506 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:48:11: 35000000 INFO @ Sat, 03 Apr 2021 08:48:18: 36000000 INFO @ Sat, 03 Apr 2021 08:48:25: 37000000 INFO @ Sat, 03 Apr 2021 08:48:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:48:32: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:48:32: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:48:32: #1 total tags in treatment: 13965934 INFO @ Sat, 03 Apr 2021 08:48:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:48:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:48:32: #1 tags after filtering in treatment: 10719397 INFO @ Sat, 03 Apr 2021 08:48:32: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 08:48:32: #1 finished! INFO @ Sat, 03 Apr 2021 08:48:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:48:33: #2 number of paired peaks: 246 WARNING @ Sat, 03 Apr 2021 08:48:33: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Sat, 03 Apr 2021 08:48:33: start model_add_line... INFO @ Sat, 03 Apr 2021 08:48:33: start X-correlation... INFO @ Sat, 03 Apr 2021 08:48:33: end of X-cor INFO @ Sat, 03 Apr 2021 08:48:33: #2 finished! INFO @ Sat, 03 Apr 2021 08:48:33: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 08:48:33: #2 alternative fragment length(s) may be 4,107,581 bps INFO @ Sat, 03 Apr 2021 08:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.20_model.r WARNING @ Sat, 03 Apr 2021 08:48:33: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:48:33: #2 You may need to consider one of the other alternative d(s): 4,107,581 WARNING @ Sat, 03 Apr 2021 08:48:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:48:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.10_summits.bed INFO @ Sat, 03 Apr 2021 08:48:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1565 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:48:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:49:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:49:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277021/SRX7277021.20_summits.bed INFO @ Sat, 03 Apr 2021 08:49:07: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (487 records, 4 fields): 2 millis CompletedMACS2peakCalling