Job ID = 6454581 SRX = SRX2325654 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:26:45 prefetch.2.10.7: 1) Downloading 'SRR4896342'... 2020-06-21T09:26:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:35:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:35:14 prefetch.2.10.7: 1) 'SRR4896342' was downloaded successfully 2020-06-21T09:35:14 prefetch.2.10.7: 'SRR4896342' has 0 unresolved dependencies Read 59033558 spots for SRR4896342/SRR4896342.sra Written 59033558 spots for SRR4896342/SRR4896342.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: 00:10:02 59033558 reads; of these: 59033558 (100.00%) were unpaired; of these: 47916618 (81.17%) aligned 0 times 8017193 (13.58%) aligned exactly 1 time 3099747 (5.25%) aligned >1 times 18.83% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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] 3325824 / 11116940 = 0.2992 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 18:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.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 18:51:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:56: 1000000 INFO @ Sun, 21 Jun 2020 18:52:02: 2000000 INFO @ Sun, 21 Jun 2020 18:52:08: 3000000 INFO @ Sun, 21 Jun 2020 18:52:14: 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 18:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.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 18:52:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:20: 5000000 INFO @ Sun, 21 Jun 2020 18:52:27: 1000000 INFO @ Sun, 21 Jun 2020 18:52:27: 6000000 INFO @ Sun, 21 Jun 2020 18:52:35: 2000000 INFO @ Sun, 21 Jun 2020 18:52:35: 7000000 INFO @ Sun, 21 Jun 2020 18:52:42: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:52:42: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:52:42: #1 total tags in treatment: 7791116 INFO @ Sun, 21 Jun 2020 18:52:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:42: #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 18:52:42: #1 tags after filtering in treatment: 7791114 INFO @ Sun, 21 Jun 2020 18:52:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:42: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:43: 3000000 INFO @ Sun, 21 Jun 2020 18:52:43: #2 number of paired peaks: 560 WARNING @ Sun, 21 Jun 2020 18:52:43: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:43: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:52:43: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 18:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.05_model.r WARNING @ Sun, 21 Jun 2020 18:52:43: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:43: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 18:52:43: #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 18:52:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:43: #3 Pre-compute pvalue-qvalue table... 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 18:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.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 18:52:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:50: 4000000 INFO @ Sun, 21 Jun 2020 18:52:58: 1000000 INFO @ Sun, 21 Jun 2020 18:52:58: 5000000 INFO @ Sun, 21 Jun 2020 18:53:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:05: 2000000 INFO @ Sun, 21 Jun 2020 18:53:06: 6000000 INFO @ Sun, 21 Jun 2020 18:53:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.05_summits.bed INFO @ Sun, 21 Jun 2020 18:53:10: Done! pass1 - making usageList (646 chroms): 1 millis pass2 - checking and writing primary data (1753 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:13: 3000000 INFO @ Sun, 21 Jun 2020 18:53:15: 7000000 INFO @ Sun, 21 Jun 2020 18:53:21: 4000000 INFO @ Sun, 21 Jun 2020 18:53:22: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:53:22: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:53:22: #1 total tags in treatment: 7791116 INFO @ Sun, 21 Jun 2020 18:53:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:22: #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 18:53:22: #1 tags after filtering in treatment: 7791114 INFO @ Sun, 21 Jun 2020 18:53:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:23: #2 number of paired peaks: 560 WARNING @ Sun, 21 Jun 2020 18:53:23: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Sun, 21 Jun 2020 18:53:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:23: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:53:23: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 18:53:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.10_model.r WARNING @ Sun, 21 Jun 2020 18:53:23: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:23: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 18:53:23: #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 18:53:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:28: 5000000 INFO @ Sun, 21 Jun 2020 18:53:36: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:43: 7000000 INFO @ Sun, 21 Jun 2020 18:53:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.10_summits.bed INFO @ Sun, 21 Jun 2020 18:53:48: Done! pass1 - making usageList (427 chroms): 1 millis pass2 - checking and writing primary data (1003 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:49: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:53:49: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:53:49: #1 total tags in treatment: 7791116 INFO @ Sun, 21 Jun 2020 18:53:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:49: #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 18:53:50: #1 tags after filtering in treatment: 7791114 INFO @ Sun, 21 Jun 2020 18:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:50: #2 number of paired peaks: 560 WARNING @ Sun, 21 Jun 2020 18:53:50: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Sun, 21 Jun 2020 18:53:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:50: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 18:53:50: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 18:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.20_model.r WARNING @ Sun, 21 Jun 2020 18:53:50: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:50: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 18:53:50: #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 18:53:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:54:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325654/SRX2325654.20_summits.bed INFO @ Sun, 21 Jun 2020 18:54:15: Done! pass1 - making usageList (224 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 9 millis CompletedMACS2peakCalling