Job ID = 6453708 SRX = SRX1433354 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:32 prefetch.2.10.7: 1) Downloading 'SRR2919819'... 2020-06-21T08:40:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:06 prefetch.2.10.7: 'SRR2919819' is valid 2020-06-21T08:43:06 prefetch.2.10.7: 1) 'SRR2919819' was downloaded successfully Read 14386095 spots for SRR2919819/SRR2919819.sra Written 14386095 spots for SRR2919819/SRR2919819.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: 00:03:58 14386095 reads; of these: 14386095 (100.00%) were unpaired; of these: 346647 (2.41%) aligned 0 times 10921243 (75.92%) aligned exactly 1 time 3118205 (21.68%) aligned >1 times 97.59% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 2097162 / 14039448 = 0.1494 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 17:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.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 17:50:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:51: 1000000 INFO @ Sun, 21 Jun 2020 17:50:58: 2000000 INFO @ Sun, 21 Jun 2020 17:51:05: 3000000 INFO @ Sun, 21 Jun 2020 17:51:11: 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 17:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.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 17:51:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:18: 5000000 INFO @ Sun, 21 Jun 2020 17:51:22: 1000000 INFO @ Sun, 21 Jun 2020 17:51:25: 6000000 INFO @ Sun, 21 Jun 2020 17:51:29: 2000000 INFO @ Sun, 21 Jun 2020 17:51:33: 7000000 INFO @ Sun, 21 Jun 2020 17:51:37: 3000000 INFO @ Sun, 21 Jun 2020 17:51:40: 8000000 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 17:51:44: 4000000 INFO @ Sun, 21 Jun 2020 17:51:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.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 17:51:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:51:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:51:47: 9000000 INFO @ Sun, 21 Jun 2020 17:51:51: 5000000 INFO @ Sun, 21 Jun 2020 17:51:52: 1000000 INFO @ Sun, 21 Jun 2020 17:51:54: 10000000 INFO @ Sun, 21 Jun 2020 17:51:59: 6000000 INFO @ Sun, 21 Jun 2020 17:51:59: 2000000 INFO @ Sun, 21 Jun 2020 17:52:02: 11000000 INFO @ Sun, 21 Jun 2020 17:52:06: 7000000 INFO @ Sun, 21 Jun 2020 17:52:07: 3000000 INFO @ Sun, 21 Jun 2020 17:52:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:52:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:52:09: #1 total tags in treatment: 11942286 INFO @ Sun, 21 Jun 2020 17:52:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:09: #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 17:52:09: #1 tags after filtering in treatment: 11942195 INFO @ Sun, 21 Jun 2020 17:52:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:10: #2 number of paired peaks: 267 WARNING @ Sun, 21 Jun 2020 17:52:10: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sun, 21 Jun 2020 17:52:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:10: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 17:52:10: #2 alternative fragment length(s) may be 4,60,598 bps INFO @ Sun, 21 Jun 2020 17:52:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.05_model.r WARNING @ Sun, 21 Jun 2020 17:52:10: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:10: #2 You may need to consider one of the other alternative d(s): 4,60,598 WARNING @ Sun, 21 Jun 2020 17:52:10: #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 17:52:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:14: 8000000 INFO @ Sun, 21 Jun 2020 17:52:14: 4000000 INFO @ Sun, 21 Jun 2020 17:52:21: 9000000 INFO @ Sun, 21 Jun 2020 17:52:21: 5000000 INFO @ Sun, 21 Jun 2020 17:52:28: 6000000 INFO @ Sun, 21 Jun 2020 17:52:28: 10000000 INFO @ Sun, 21 Jun 2020 17:52:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:35: 7000000 INFO @ Sun, 21 Jun 2020 17:52:36: 11000000 INFO @ Sun, 21 Jun 2020 17:52:42: 8000000 INFO @ Sun, 21 Jun 2020 17:52:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:52:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:52:43: #1 total tags in treatment: 11942286 INFO @ Sun, 21 Jun 2020 17:52:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:43: #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 17:52:43: #1 tags after filtering in treatment: 11942195 INFO @ Sun, 21 Jun 2020 17:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:44: #2 number of paired peaks: 267 WARNING @ Sun, 21 Jun 2020 17:52:44: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sun, 21 Jun 2020 17:52:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:44: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 17:52:44: #2 alternative fragment length(s) may be 4,60,598 bps INFO @ Sun, 21 Jun 2020 17:52:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.10_model.r WARNING @ Sun, 21 Jun 2020 17:52:44: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:44: #2 You may need to consider one of the other alternative d(s): 4,60,598 WARNING @ Sun, 21 Jun 2020 17:52:44: #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 17:52:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.05_summits.bed INFO @ Sun, 21 Jun 2020 17:52:44: Done! pass1 - making usageList (224 chroms): 2 millis pass2 - checking and writing primary data (812 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:49: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:52:56: 10000000 INFO @ Sun, 21 Jun 2020 17:53:02: 11000000 INFO @ Sun, 21 Jun 2020 17:53:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:53:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:53:08: #1 total tags in treatment: 11942286 INFO @ Sun, 21 Jun 2020 17:53:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:08: #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 17:53:09: #1 tags after filtering in treatment: 11942195 INFO @ Sun, 21 Jun 2020 17:53:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:10: #2 number of paired peaks: 267 WARNING @ Sun, 21 Jun 2020 17:53:10: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Sun, 21 Jun 2020 17:53:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:10: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 17:53:10: #2 alternative fragment length(s) may be 4,60,598 bps INFO @ Sun, 21 Jun 2020 17:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.20_model.r WARNING @ Sun, 21 Jun 2020 17:53:10: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:10: #2 You may need to consider one of the other alternative d(s): 4,60,598 WARNING @ Sun, 21 Jun 2020 17:53:10: #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 17:53:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.10_summits.bed INFO @ Sun, 21 Jun 2020 17:53:19: Done! pass1 - making usageList (119 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433354/SRX1433354.20_summits.bed INFO @ Sun, 21 Jun 2020 17:53:44: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling