Job ID = 6458074 SRX = SRX495201 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:23:19 prefetch.2.10.7: 1) Downloading 'SRR1198706'... 2020-06-21T12:23:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:25:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:25:17 prefetch.2.10.7: 'SRR1198706' is valid 2020-06-21T12:25:17 prefetch.2.10.7: 1) 'SRR1198706' was downloaded successfully Read 17633613 spots for SRR1198706/SRR1198706.sra Written 17633613 spots for SRR1198706/SRR1198706.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: 00:05:53 17633613 reads; of these: 17633613 (100.00%) were unpaired; of these: 244036 (1.38%) aligned 0 times 11965835 (67.86%) aligned exactly 1 time 5423742 (30.76%) aligned >1 times 98.62% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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 8 files... [bam_rmdupse_core] 4290057 / 17389577 = 0.2467 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 21:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.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 21:37:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:36: 1000000 INFO @ Sun, 21 Jun 2020 21:37:43: 2000000 INFO @ Sun, 21 Jun 2020 21:37:50: 3000000 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 21:37:57: 4000000 INFO @ Sun, 21 Jun 2020 21:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.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 21:37:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:38:04: 5000000 INFO @ Sun, 21 Jun 2020 21:38:06: 1000000 INFO @ Sun, 21 Jun 2020 21:38:12: 6000000 INFO @ Sun, 21 Jun 2020 21:38:13: 2000000 INFO @ Sun, 21 Jun 2020 21:38:19: 7000000 INFO @ Sun, 21 Jun 2020 21:38:20: 3000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 21:38:27: 8000000 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 21:38:27: 4000000 INFO @ Sun, 21 Jun 2020 21:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.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 21:38:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:38:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:38:33: 5000000 INFO @ Sun, 21 Jun 2020 21:38:35: 9000000 INFO @ Sun, 21 Jun 2020 21:38:38: 1000000 INFO @ Sun, 21 Jun 2020 21:38:40: 6000000 INFO @ Sun, 21 Jun 2020 21:38:44: 10000000 INFO @ Sun, 21 Jun 2020 21:38:46: 2000000 INFO @ Sun, 21 Jun 2020 21:38:47: 7000000 INFO @ Sun, 21 Jun 2020 21:38:53: 11000000 INFO @ Sun, 21 Jun 2020 21:38:54: 3000000 INFO @ Sun, 21 Jun 2020 21:38:54: 8000000 INFO @ Sun, 21 Jun 2020 21:39:01: 12000000 INFO @ Sun, 21 Jun 2020 21:39:02: 9000000 INFO @ Sun, 21 Jun 2020 21:39:03: 4000000 INFO @ Sun, 21 Jun 2020 21:39:10: 13000000 INFO @ Sun, 21 Jun 2020 21:39:10: 10000000 INFO @ Sun, 21 Jun 2020 21:39:11: 5000000 INFO @ Sun, 21 Jun 2020 21:39:11: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:39:11: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:39:11: #1 total tags in treatment: 13099520 INFO @ Sun, 21 Jun 2020 21:39:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:39:11: #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 21:39:11: #1 tags after filtering in treatment: 13099519 INFO @ Sun, 21 Jun 2020 21:39:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:39:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:39:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:39:12: #2 number of paired peaks: 265 WARNING @ Sun, 21 Jun 2020 21:39:12: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 21 Jun 2020 21:39:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:39:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:39:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:39:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:39:12: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:39:12: #2 alternative fragment length(s) may be 3,11,32 bps INFO @ Sun, 21 Jun 2020 21:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.05_model.r WARNING @ Sun, 21 Jun 2020 21:39:12: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:39:12: #2 You may need to consider one of the other alternative d(s): 3,11,32 WARNING @ Sun, 21 Jun 2020 21:39:12: #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 21:39:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:39:18: 11000000 INFO @ Sun, 21 Jun 2020 21:39:18: 6000000 INFO @ Sun, 21 Jun 2020 21:39:25: 12000000 INFO @ Sun, 21 Jun 2020 21:39:26: 7000000 INFO @ Sun, 21 Jun 2020 21:39:32: 13000000 INFO @ Sun, 21 Jun 2020 21:39:33: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:39:33: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:39:33: #1 total tags in treatment: 13099520 INFO @ Sun, 21 Jun 2020 21:39:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:39:33: #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 21:39:34: #1 tags after filtering in treatment: 13099519 INFO @ Sun, 21 Jun 2020 21:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:39:34: #1 finished! INFO @ Sun, 21 Jun 2020 21:39:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:39:34: 8000000 INFO @ Sun, 21 Jun 2020 21:39:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:39:35: #2 number of paired peaks: 265 WARNING @ Sun, 21 Jun 2020 21:39:35: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 21 Jun 2020 21:39:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:39:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:39:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:39:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:39:35: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:39:35: #2 alternative fragment length(s) may be 3,11,32 bps INFO @ Sun, 21 Jun 2020 21:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.10_model.r WARNING @ Sun, 21 Jun 2020 21:39:35: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:39:35: #2 You may need to consider one of the other alternative d(s): 3,11,32 WARNING @ Sun, 21 Jun 2020 21:39:35: #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 21:39:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:39:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:39:42: 9000000 INFO @ Sun, 21 Jun 2020 21:39:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:39:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:39:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.05_summits.bed INFO @ Sun, 21 Jun 2020 21:39:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:39:50: 10000000 INFO @ Sun, 21 Jun 2020 21:39:58: 11000000 INFO @ Sun, 21 Jun 2020 21:39:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:40:05: 12000000 INFO @ Sun, 21 Jun 2020 21:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:40:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.10_summits.bed INFO @ Sun, 21 Jun 2020 21:40:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:40:13: 13000000 INFO @ Sun, 21 Jun 2020 21:40:14: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:40:14: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:40:14: #1 total tags in treatment: 13099520 INFO @ Sun, 21 Jun 2020 21:40:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:14: #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 21:40:14: #1 tags after filtering in treatment: 13099519 INFO @ Sun, 21 Jun 2020 21:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:15: #2 number of paired peaks: 265 WARNING @ Sun, 21 Jun 2020 21:40:15: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Sun, 21 Jun 2020 21:40:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:15: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:15: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:15: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:15: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 21:40:15: #2 alternative fragment length(s) may be 3,11,32 bps INFO @ Sun, 21 Jun 2020 21:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.20_model.r WARNING @ Sun, 21 Jun 2020 21:40:15: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:40:15: #2 You may need to consider one of the other alternative d(s): 3,11,32 WARNING @ Sun, 21 Jun 2020 21:40:15: #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 21:40:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:40:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:40:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:40:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:40:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495201/SRX495201.20_summits.bed INFO @ Sun, 21 Jun 2020 21:40:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling