Job ID = 6456868 SRX = SRX403436 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:13:09 prefetch.2.10.7: 1) Downloading 'SRR1066651'... 2020-06-21T11:13:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:16:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:16:47 prefetch.2.10.7: 1) 'SRR1066651' was downloaded successfully Read 37277198 spots for SRR1066651/SRR1066651.sra Written 37277198 spots for SRR1066651/SRR1066651.sra 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: 00:11:03 37277198 reads; of these: 37277198 (100.00%) were unpaired; of these: 2105072 (5.65%) aligned 0 times 22742942 (61.01%) aligned exactly 1 time 12429184 (33.34%) aligned >1 times 94.35% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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] 12461673 / 35172126 = 0.3543 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.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 @ Sun, 21 Jun 2020 20:37:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:37:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:21: 1000000 INFO @ Sun, 21 Jun 2020 20:37:28: 2000000 INFO @ Sun, 21 Jun 2020 20:37:34: 3000000 INFO @ Sun, 21 Jun 2020 20:37:40: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.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 @ Sun, 21 Jun 2020 20:37:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:37:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:46: 5000000 INFO @ Sun, 21 Jun 2020 20:37:52: 1000000 INFO @ Sun, 21 Jun 2020 20:37:53: 6000000 INFO @ Sun, 21 Jun 2020 20:37:59: 2000000 INFO @ Sun, 21 Jun 2020 20:38:00: 7000000 INFO @ Sun, 21 Jun 2020 20:38:05: 3000000 INFO @ Sun, 21 Jun 2020 20:38:06: 8000000 INFO @ Sun, 21 Jun 2020 20:38:12: 4000000 INFO @ Sun, 21 Jun 2020 20:38:13: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.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 @ Sun, 21 Jun 2020 20:38:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:18: 5000000 INFO @ Sun, 21 Jun 2020 20:38:20: 10000000 INFO @ Sun, 21 Jun 2020 20:38:22: 1000000 INFO @ Sun, 21 Jun 2020 20:38:25: 6000000 INFO @ Sun, 21 Jun 2020 20:38:27: 11000000 INFO @ Sun, 21 Jun 2020 20:38:29: 2000000 INFO @ Sun, 21 Jun 2020 20:38:32: 7000000 INFO @ Sun, 21 Jun 2020 20:38:34: 12000000 INFO @ Sun, 21 Jun 2020 20:38:35: 3000000 INFO @ Sun, 21 Jun 2020 20:38:39: 8000000 INFO @ Sun, 21 Jun 2020 20:38:41: 13000000 INFO @ Sun, 21 Jun 2020 20:38:42: 4000000 INFO @ Sun, 21 Jun 2020 20:38:45: 9000000 INFO @ Sun, 21 Jun 2020 20:38:48: 14000000 INFO @ Sun, 21 Jun 2020 20:38:49: 5000000 INFO @ Sun, 21 Jun 2020 20:38:52: 10000000 INFO @ Sun, 21 Jun 2020 20:38:55: 15000000 INFO @ Sun, 21 Jun 2020 20:38:56: 6000000 INFO @ Sun, 21 Jun 2020 20:38:59: 11000000 INFO @ Sun, 21 Jun 2020 20:39:02: 7000000 INFO @ Sun, 21 Jun 2020 20:39:02: 16000000 INFO @ Sun, 21 Jun 2020 20:39:05: 12000000 INFO @ Sun, 21 Jun 2020 20:39:09: 8000000 INFO @ Sun, 21 Jun 2020 20:39:09: 17000000 INFO @ Sun, 21 Jun 2020 20:39:12: 13000000 INFO @ Sun, 21 Jun 2020 20:39:15: 9000000 INFO @ Sun, 21 Jun 2020 20:39:17: 18000000 INFO @ Sun, 21 Jun 2020 20:39:19: 14000000 INFO @ Sun, 21 Jun 2020 20:39:22: 10000000 INFO @ Sun, 21 Jun 2020 20:39:25: 19000000 INFO @ Sun, 21 Jun 2020 20:39:26: 15000000 INFO @ Sun, 21 Jun 2020 20:39:29: 11000000 INFO @ Sun, 21 Jun 2020 20:39:32: 20000000 INFO @ Sun, 21 Jun 2020 20:39:32: 16000000 INFO @ Sun, 21 Jun 2020 20:39:35: 12000000 INFO @ Sun, 21 Jun 2020 20:39:39: 17000000 INFO @ Sun, 21 Jun 2020 20:39:39: 21000000 INFO @ Sun, 21 Jun 2020 20:39:42: 13000000 INFO @ Sun, 21 Jun 2020 20:39:46: 18000000 INFO @ Sun, 21 Jun 2020 20:39:47: 22000000 INFO @ Sun, 21 Jun 2020 20:39:49: 14000000 INFO @ Sun, 21 Jun 2020 20:39:52: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:39:52: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:39:52: #1 total tags in treatment: 22710453 INFO @ Sun, 21 Jun 2020 20:39:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:39:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:39:53: 19000000 INFO @ Sun, 21 Jun 2020 20:39:53: #1 tags after filtering in treatment: 22710452 INFO @ Sun, 21 Jun 2020 20:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:39:53: #1 finished! INFO @ Sun, 21 Jun 2020 20:39:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:39:55: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 20:39:55: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 20:39:55: start model_add_line... INFO @ Sun, 21 Jun 2020 20:39:55: start X-correlation... INFO @ Sun, 21 Jun 2020 20:39:55: end of X-cor INFO @ Sun, 21 Jun 2020 20:39:55: #2 finished! INFO @ Sun, 21 Jun 2020 20:39:55: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:39:55: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 20:39:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.05_model.r WARNING @ Sun, 21 Jun 2020 20:39:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:39:55: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 20:39:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:39:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:39:55: 15000000 INFO @ Sun, 21 Jun 2020 20:39:59: 20000000 INFO @ Sun, 21 Jun 2020 20:40:02: 16000000 INFO @ Sun, 21 Jun 2020 20:40:06: 21000000 INFO @ Sun, 21 Jun 2020 20:40:08: 17000000 INFO @ Sun, 21 Jun 2020 20:40:13: 22000000 INFO @ Sun, 21 Jun 2020 20:40:15: 18000000 INFO @ Sun, 21 Jun 2020 20:40:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:40:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:40:17: #1 total tags in treatment: 22710453 INFO @ Sun, 21 Jun 2020 20:40:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:40:18: #1 tags after filtering in treatment: 22710452 INFO @ Sun, 21 Jun 2020 20:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:20: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 20:40:20: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 20:40:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:20: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:20: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:20: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:40:20: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 20:40:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.10_model.r WARNING @ Sun, 21 Jun 2020 20:40:20: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:40:20: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 20:40:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:40:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:21: 19000000 INFO @ Sun, 21 Jun 2020 20:40:27: 20000000 INFO @ Sun, 21 Jun 2020 20:40:33: 21000000 INFO @ Sun, 21 Jun 2020 20:40:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:39: 22000000 INFO @ Sun, 21 Jun 2020 20:40:44: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:40:44: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:40:44: #1 total tags in treatment: 22710453 INFO @ Sun, 21 Jun 2020 20:40:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:40:44: #1 tags after filtering in treatment: 22710452 INFO @ Sun, 21 Jun 2020 20:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:44: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:46: #2 number of paired peaks: 860 WARNING @ Sun, 21 Jun 2020 20:40:46: Fewer paired peaks (860) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 860 pairs to build model! INFO @ Sun, 21 Jun 2020 20:40:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:46: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:40:46: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 20:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.20_model.r WARNING @ Sun, 21 Jun 2020 20:40:46: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:40:46: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 20:40:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:40:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:40:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.05_summits.bed INFO @ Sun, 21 Jun 2020 20:40:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:40:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.10_summits.bed INFO @ Sun, 21 Jun 2020 20:41:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:41:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX403436/SRX403436.20_summits.bed INFO @ Sun, 21 Jun 2020 20:41:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling