Job ID = 6455385 SRX = SRX287745 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:55:25 prefetch.2.10.7: 1) Downloading 'SRR869934'... 2020-06-21T09:55:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:58:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:58:58 prefetch.2.10.7: 1) 'SRR869934' was downloaded successfully Read 17355751 spots for SRR869934/SRR869934.sra Written 17355751 spots for SRR869934/SRR869934.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: 00:05:10 17355751 reads; of these: 17355751 (100.00%) were unpaired; of these: 1248875 (7.20%) aligned 0 times 10894703 (62.77%) aligned exactly 1 time 5212173 (30.03%) aligned >1 times 92.80% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 3083661 / 16106876 = 0.1914 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 19:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.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 19:09:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:17: 1000000 INFO @ Sun, 21 Jun 2020 19:09:22: 2000000 INFO @ Sun, 21 Jun 2020 19:09:28: 3000000 INFO @ Sun, 21 Jun 2020 19:09:33: 4000000 INFO @ Sun, 21 Jun 2020 19:09:39: 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 19:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.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 19:09:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:44: 6000000 INFO @ Sun, 21 Jun 2020 19:09:47: 1000000 INFO @ Sun, 21 Jun 2020 19:09:50: 7000000 INFO @ Sun, 21 Jun 2020 19:09:52: 2000000 INFO @ Sun, 21 Jun 2020 19:09:56: 8000000 INFO @ Sun, 21 Jun 2020 19:09:57: 3000000 INFO @ Sun, 21 Jun 2020 19:10:02: 9000000 INFO @ Sun, 21 Jun 2020 19:10:02: 4000000 INFO @ Sun, 21 Jun 2020 19:10:07: 5000000 INFO @ Sun, 21 Jun 2020 19:10:07: 10000000 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 19:10:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.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 19:10:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:12: 6000000 INFO @ Sun, 21 Jun 2020 19:10:14: 11000000 INFO @ Sun, 21 Jun 2020 19:10:17: 1000000 INFO @ Sun, 21 Jun 2020 19:10:17: 7000000 INFO @ Sun, 21 Jun 2020 19:10:19: 12000000 INFO @ Sun, 21 Jun 2020 19:10:22: 2000000 INFO @ Sun, 21 Jun 2020 19:10:23: 8000000 INFO @ Sun, 21 Jun 2020 19:10:25: 13000000 INFO @ Sun, 21 Jun 2020 19:10:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:26: #1 total tags in treatment: 13023215 INFO @ Sun, 21 Jun 2020 19:10:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:26: #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 19:10:26: #1 tags after filtering in treatment: 13023215 INFO @ Sun, 21 Jun 2020 19:10:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:27: #2 number of paired peaks: 846 WARNING @ Sun, 21 Jun 2020 19:10:27: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:27: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:10:27: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.05_model.r WARNING @ Sun, 21 Jun 2020 19:10:27: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:27: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:10:27: #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 19:10:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:27: 3000000 INFO @ Sun, 21 Jun 2020 19:10:28: 9000000 INFO @ Sun, 21 Jun 2020 19:10:32: 4000000 INFO @ Sun, 21 Jun 2020 19:10:33: 10000000 INFO @ Sun, 21 Jun 2020 19:10:38: 5000000 INFO @ Sun, 21 Jun 2020 19:10:39: 11000000 INFO @ Sun, 21 Jun 2020 19:10:43: 6000000 INFO @ Sun, 21 Jun 2020 19:10:44: 12000000 INFO @ Sun, 21 Jun 2020 19:10:48: 7000000 INFO @ Sun, 21 Jun 2020 19:10:50: 13000000 INFO @ Sun, 21 Jun 2020 19:10:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:50: #1 total tags in treatment: 13023215 INFO @ Sun, 21 Jun 2020 19:10:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:50: #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 19:10:50: #1 tags after filtering in treatment: 13023215 INFO @ Sun, 21 Jun 2020 19:10:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:51: #2 number of paired peaks: 846 WARNING @ Sun, 21 Jun 2020 19:10:51: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:51: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:10:51: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.10_model.r WARNING @ Sun, 21 Jun 2020 19:10:51: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:51: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:10:51: #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 19:10:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:53: 8000000 INFO @ Sun, 21 Jun 2020 19:10:58: 9000000 INFO @ Sun, 21 Jun 2020 19:11:03: 10000000 INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.05_summits.bed INFO @ Sun, 21 Jun 2020 19:11:04: Done! pass1 - making usageList (648 chroms): 1 millis pass2 - checking and writing primary data (2352 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:09: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:11:14: 12000000 INFO @ Sun, 21 Jun 2020 19:11:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:19: 13000000 INFO @ Sun, 21 Jun 2020 19:11:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:11:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:11:19: #1 total tags in treatment: 13023215 INFO @ Sun, 21 Jun 2020 19:11:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:19: #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 19:11:20: #1 tags after filtering in treatment: 13023215 INFO @ Sun, 21 Jun 2020 19:11:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:21: #2 number of paired peaks: 846 WARNING @ Sun, 21 Jun 2020 19:11:21: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Sun, 21 Jun 2020 19:11:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:21: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:11:21: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.20_model.r WARNING @ Sun, 21 Jun 2020 19:11:21: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:21: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:11:21: #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 19:11:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.10_summits.bed INFO @ Sun, 21 Jun 2020 19:11:29: Done! pass1 - making usageList (524 chroms): 1 millis pass2 - checking and writing primary data (2015 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:11:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287745/SRX287745.20_summits.bed INFO @ Sun, 21 Jun 2020 19:11:57: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (1122 records, 4 fields): 12 millis CompletedMACS2peakCalling