Job ID = 6456021 SRX = SRX3159478 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:36:59 prefetch.2.10.7: 1) Downloading 'SRR6004208'... 2020-06-21T10:36:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:13 prefetch.2.10.7: 'SRR6004208' is valid 2020-06-21T10:41:13 prefetch.2.10.7: 1) 'SRR6004208' was downloaded successfully 2020-06-21T10:41:13 prefetch.2.10.7: 'SRR6004208' has 0 unresolved dependencies Read 28942927 spots for SRR6004208/SRR6004208.sra Written 28942927 spots for SRR6004208/SRR6004208.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: 00:08:46 28942927 reads; of these: 28942927 (100.00%) were unpaired; of these: 953665 (3.29%) aligned 0 times 19468782 (67.27%) aligned exactly 1 time 8520480 (29.44%) aligned >1 times 96.71% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 4399966 / 27989262 = 0.1572 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 19:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.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 19:58:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:21: 1000000 INFO @ Sun, 21 Jun 2020 19:58:26: 2000000 INFO @ Sun, 21 Jun 2020 19:58:32: 3000000 INFO @ Sun, 21 Jun 2020 19:58:37: 4000000 INFO @ Sun, 21 Jun 2020 19:58:42: 5000000 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 19:58:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.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 19:58:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:48: 6000000 INFO @ Sun, 21 Jun 2020 19:58:52: 1000000 INFO @ Sun, 21 Jun 2020 19:58:53: 7000000 INFO @ Sun, 21 Jun 2020 19:58:58: 2000000 INFO @ Sun, 21 Jun 2020 19:58:59: 8000000 INFO @ Sun, 21 Jun 2020 19:59:04: 3000000 INFO @ Sun, 21 Jun 2020 19:59:04: 9000000 INFO @ Sun, 21 Jun 2020 19:59:10: 10000000 INFO @ Sun, 21 Jun 2020 19:59:10: 4000000 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 19:59:16: 11000000 INFO @ Sun, 21 Jun 2020 19:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.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 19:59:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:59:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:59:16: 5000000 INFO @ Sun, 21 Jun 2020 19:59:22: 12000000 INFO @ Sun, 21 Jun 2020 19:59:22: 1000000 INFO @ Sun, 21 Jun 2020 19:59:22: 6000000 INFO @ Sun, 21 Jun 2020 19:59:28: 13000000 INFO @ Sun, 21 Jun 2020 19:59:28: 7000000 INFO @ Sun, 21 Jun 2020 19:59:28: 2000000 INFO @ Sun, 21 Jun 2020 19:59:34: 14000000 INFO @ Sun, 21 Jun 2020 19:59:34: 8000000 INFO @ Sun, 21 Jun 2020 19:59:34: 3000000 INFO @ Sun, 21 Jun 2020 19:59:40: 15000000 INFO @ Sun, 21 Jun 2020 19:59:40: 9000000 INFO @ Sun, 21 Jun 2020 19:59:41: 4000000 INFO @ Sun, 21 Jun 2020 19:59:46: 10000000 INFO @ Sun, 21 Jun 2020 19:59:46: 16000000 INFO @ Sun, 21 Jun 2020 19:59:47: 5000000 INFO @ Sun, 21 Jun 2020 19:59:52: 11000000 INFO @ Sun, 21 Jun 2020 19:59:53: 17000000 INFO @ Sun, 21 Jun 2020 19:59:53: 6000000 INFO @ Sun, 21 Jun 2020 19:59:58: 12000000 INFO @ Sun, 21 Jun 2020 19:59:59: 18000000 INFO @ Sun, 21 Jun 2020 20:00:00: 7000000 INFO @ Sun, 21 Jun 2020 20:00:04: 13000000 INFO @ Sun, 21 Jun 2020 20:00:05: 19000000 INFO @ Sun, 21 Jun 2020 20:00:06: 8000000 INFO @ Sun, 21 Jun 2020 20:00:10: 14000000 INFO @ Sun, 21 Jun 2020 20:00:12: 9000000 INFO @ Sun, 21 Jun 2020 20:00:12: 20000000 INFO @ Sun, 21 Jun 2020 20:00:16: 15000000 INFO @ Sun, 21 Jun 2020 20:00:18: 10000000 INFO @ Sun, 21 Jun 2020 20:00:18: 21000000 INFO @ Sun, 21 Jun 2020 20:00:21: 16000000 INFO @ Sun, 21 Jun 2020 20:00:24: 11000000 INFO @ Sun, 21 Jun 2020 20:00:24: 22000000 INFO @ Sun, 21 Jun 2020 20:00:27: 17000000 INFO @ Sun, 21 Jun 2020 20:00:30: 12000000 INFO @ Sun, 21 Jun 2020 20:00:31: 23000000 INFO @ Sun, 21 Jun 2020 20:00:33: 18000000 INFO @ Sun, 21 Jun 2020 20:00:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:00:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:00:35: #1 total tags in treatment: 23589296 INFO @ Sun, 21 Jun 2020 20:00:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:35: #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 20:00:36: 13000000 INFO @ Sun, 21 Jun 2020 20:00:36: #1 tags after filtering in treatment: 23589296 INFO @ Sun, 21 Jun 2020 20:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:38: #2 number of paired peaks: 429 WARNING @ Sun, 21 Jun 2020 20:00:38: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:38: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:00:38: #2 alternative fragment length(s) may be 2,28 bps INFO @ Sun, 21 Jun 2020 20:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.05_model.r WARNING @ Sun, 21 Jun 2020 20:00:38: #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 20:00:38: #2 You may need to consider one of the other alternative d(s): 2,28 WARNING @ Sun, 21 Jun 2020 20:00:38: #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 20:00:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:40: 19000000 INFO @ Sun, 21 Jun 2020 20:00:41: 14000000 INFO @ Sun, 21 Jun 2020 20:00:46: 20000000 INFO @ Sun, 21 Jun 2020 20:00:47: 15000000 INFO @ Sun, 21 Jun 2020 20:00:51: 21000000 INFO @ Sun, 21 Jun 2020 20:00:53: 16000000 INFO @ Sun, 21 Jun 2020 20:00:57: 22000000 INFO @ Sun, 21 Jun 2020 20:00:58: 17000000 INFO @ Sun, 21 Jun 2020 20:01:03: 23000000 INFO @ Sun, 21 Jun 2020 20:01:03: 18000000 INFO @ Sun, 21 Jun 2020 20:01:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:01:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:01:07: #1 total tags in treatment: 23589296 INFO @ Sun, 21 Jun 2020 20:01:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:01:07: #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 20:01:08: #1 tags after filtering in treatment: 23589296 INFO @ Sun, 21 Jun 2020 20:01:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:01:08: #1 finished! INFO @ Sun, 21 Jun 2020 20:01:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:01:10: 19000000 INFO @ Sun, 21 Jun 2020 20:01:10: #2 number of paired peaks: 429 WARNING @ Sun, 21 Jun 2020 20:01:10: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 21 Jun 2020 20:01:10: start model_add_line... INFO @ Sun, 21 Jun 2020 20:01:10: start X-correlation... INFO @ Sun, 21 Jun 2020 20:01:10: end of X-cor INFO @ Sun, 21 Jun 2020 20:01:10: #2 finished! INFO @ Sun, 21 Jun 2020 20:01:10: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:01:10: #2 alternative fragment length(s) may be 2,28 bps INFO @ Sun, 21 Jun 2020 20:01:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.10_model.r WARNING @ Sun, 21 Jun 2020 20:01:10: #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 20:01:10: #2 You may need to consider one of the other alternative d(s): 2,28 WARNING @ Sun, 21 Jun 2020 20:01:10: #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 20:01:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:01:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:01:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:15: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:01:21: 21000000 INFO @ Sun, 21 Jun 2020 20:01:26: 22000000 INFO @ Sun, 21 Jun 2020 20:01:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.05_summits.bed INFO @ Sun, 21 Jun 2020 20:01:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Sun, 21 Jun 2020 20:01:31: 23000000 CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:01:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:01:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:01:35: #1 total tags in treatment: 23589296 INFO @ Sun, 21 Jun 2020 20:01:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:01:35: #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 20:01:36: #1 tags after filtering in treatment: 23589296 INFO @ Sun, 21 Jun 2020 20:01:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:01:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:01:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:01:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:01:37: #2 number of paired peaks: 429 WARNING @ Sun, 21 Jun 2020 20:01:37: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Sun, 21 Jun 2020 20:01:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:01:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:01:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:01:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:01:38: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:01:38: #2 alternative fragment length(s) may be 2,28 bps INFO @ Sun, 21 Jun 2020 20:01:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.20_model.r WARNING @ Sun, 21 Jun 2020 20:01:38: #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 20:01:38: #2 You may need to consider one of the other alternative d(s): 2,28 WARNING @ Sun, 21 Jun 2020 20:01:38: #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 20:01:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:01:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:01:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.10_summits.bed INFO @ Sun, 21 Jun 2020 20:02:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:02:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:02:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159478/SRX3159478.20_summits.bed INFO @ Sun, 21 Jun 2020 20:02:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling