Job ID = 6459473 SRX = SRX681832 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:06:46 prefetch.2.10.7: 1) Downloading 'SRR1552301'... 2020-06-21T13:06:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:13:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:13:14 prefetch.2.10.7: 1) 'SRR1552301' was downloaded successfully Read 37866834 spots for SRR1552301/SRR1552301.sra Written 37866834 spots for SRR1552301/SRR1552301.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:43 37866834 reads; of these: 37866834 (100.00%) were unpaired; of these: 13191236 (34.84%) aligned 0 times 18959541 (50.07%) aligned exactly 1 time 5716057 (15.10%) aligned >1 times 65.16% overall alignment rate Time searching: 00:07:44 Overall time: 00:07:44 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] 17161425 / 24675598 = 0.6955 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 22:27:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.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 22:27:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:27:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:27:33: 1000000 INFO @ Sun, 21 Jun 2020 22:27:38: 2000000 INFO @ Sun, 21 Jun 2020 22:27:44: 3000000 INFO @ Sun, 21 Jun 2020 22:27:49: 4000000 INFO @ Sun, 21 Jun 2020 22:27:55: 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 22:27:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.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 22:27:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:27:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:28:01: 6000000 INFO @ Sun, 21 Jun 2020 22:28:03: 1000000 INFO @ Sun, 21 Jun 2020 22:28:07: 7000000 INFO @ Sun, 21 Jun 2020 22:28:09: 2000000 INFO @ Sun, 21 Jun 2020 22:28:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:28:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:28:11: #1 total tags in treatment: 7514173 INFO @ Sun, 21 Jun 2020 22:28:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:28:11: #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 22:28:11: #1 tags after filtering in treatment: 7514171 INFO @ Sun, 21 Jun 2020 22:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:28:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:28:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:28:12: #2 number of paired peaks: 990 WARNING @ Sun, 21 Jun 2020 22:28:12: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Sun, 21 Jun 2020 22:28:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:28:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:28:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:28:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:28:12: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:28:12: #2 alternative fragment length(s) may be 4,48,567 bps INFO @ Sun, 21 Jun 2020 22:28:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.05_model.r WARNING @ Sun, 21 Jun 2020 22:28:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:28:12: #2 You may need to consider one of the other alternative d(s): 4,48,567 WARNING @ Sun, 21 Jun 2020 22:28:12: #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 22:28:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:28:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:28:15: 3000000 INFO @ Sun, 21 Jun 2020 22:28:21: 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 22:28:27: 5000000 INFO @ Sun, 21 Jun 2020 22:28:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.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 22:28:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:28:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:28:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:28:33: 6000000 INFO @ Sun, 21 Jun 2020 22:28:33: 1000000 INFO @ Sun, 21 Jun 2020 22:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.05_summits.bed INFO @ Sun, 21 Jun 2020 22:28:35: Done! pass1 - making usageList (557 chroms): 1 millis pass2 - checking and writing primary data (2665 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:28:39: 7000000 INFO @ Sun, 21 Jun 2020 22:28:39: 2000000 INFO @ Sun, 21 Jun 2020 22:28:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:28:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:28:43: #1 total tags in treatment: 7514173 INFO @ Sun, 21 Jun 2020 22:28:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:28:43: #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 22:28:43: #1 tags after filtering in treatment: 7514171 INFO @ Sun, 21 Jun 2020 22:28:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:28:43: #1 finished! INFO @ Sun, 21 Jun 2020 22:28:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:28:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:28:44: #2 number of paired peaks: 990 WARNING @ Sun, 21 Jun 2020 22:28:44: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Sun, 21 Jun 2020 22:28:44: start model_add_line... INFO @ Sun, 21 Jun 2020 22:28:44: start X-correlation... INFO @ Sun, 21 Jun 2020 22:28:44: end of X-cor INFO @ Sun, 21 Jun 2020 22:28:44: #2 finished! INFO @ Sun, 21 Jun 2020 22:28:44: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:28:44: #2 alternative fragment length(s) may be 4,48,567 bps INFO @ Sun, 21 Jun 2020 22:28:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.10_model.r WARNING @ Sun, 21 Jun 2020 22:28:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:28:44: #2 You may need to consider one of the other alternative d(s): 4,48,567 WARNING @ Sun, 21 Jun 2020 22:28:44: #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 22:28:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:28:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:28:45: 3000000 INFO @ Sun, 21 Jun 2020 22:28:51: 4000000 INFO @ Sun, 21 Jun 2020 22:28:57: 5000000 INFO @ Sun, 21 Jun 2020 22:28:59: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:29:03: 6000000 INFO @ Sun, 21 Jun 2020 22:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.10_summits.bed INFO @ Sun, 21 Jun 2020 22:29:06: Done! pass1 - making usageList (467 chroms): 1 millis pass2 - checking and writing primary data (1655 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:29:09: 7000000 INFO @ Sun, 21 Jun 2020 22:29:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:29:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:29:12: #1 total tags in treatment: 7514173 INFO @ Sun, 21 Jun 2020 22:29:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:29:12: #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 22:29:12: #1 tags after filtering in treatment: 7514171 INFO @ Sun, 21 Jun 2020 22:29:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:29:12: #1 finished! INFO @ Sun, 21 Jun 2020 22:29:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:29:13: #2 number of paired peaks: 990 WARNING @ Sun, 21 Jun 2020 22:29:13: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Sun, 21 Jun 2020 22:29:13: start model_add_line... INFO @ Sun, 21 Jun 2020 22:29:13: start X-correlation... INFO @ Sun, 21 Jun 2020 22:29:13: end of X-cor INFO @ Sun, 21 Jun 2020 22:29:13: #2 finished! INFO @ Sun, 21 Jun 2020 22:29:13: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:29:13: #2 alternative fragment length(s) may be 4,48,567 bps INFO @ Sun, 21 Jun 2020 22:29:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.20_model.r WARNING @ Sun, 21 Jun 2020 22:29:13: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:29:13: #2 You may need to consider one of the other alternative d(s): 4,48,567 WARNING @ Sun, 21 Jun 2020 22:29:13: #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 22:29:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:29:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:29:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681832/SRX681832.20_summits.bed INFO @ Sun, 21 Jun 2020 22:29:36: Done! pass1 - making usageList (242 chroms): 1 millis pass2 - checking and writing primary data (499 records, 4 fields): 7 millis CompletedMACS2peakCalling