Job ID = 6456255 SRX = SRX331407 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:36:30 prefetch.2.10.7: 1) Downloading 'SRR947644'... 2020-06-21T10:36:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:53 prefetch.2.10.7: 'SRR947644' is valid 2020-06-21T10:37:53 prefetch.2.10.7: 1) 'SRR947644' was downloaded successfully Read 10855678 spots for SRR947644/SRR947644.sra Written 10855678 spots for SRR947644/SRR947644.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: 00:02:29 10855678 reads; of these: 10855678 (100.00%) were unpaired; of these: 614619 (5.66%) aligned 0 times 8761451 (80.71%) aligned exactly 1 time 1479608 (13.63%) aligned >1 times 94.34% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 907367 / 10241059 = 0.0886 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 19:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.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 19:43:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:01: 1000000 INFO @ Sun, 21 Jun 2020 19:44:07: 2000000 INFO @ Sun, 21 Jun 2020 19:44:13: 3000000 INFO @ Sun, 21 Jun 2020 19:44:19: 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 19:44:25: 5000000 INFO @ Sun, 21 Jun 2020 19:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.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 19:44:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:32: 6000000 INFO @ Sun, 21 Jun 2020 19:44:32: 1000000 INFO @ Sun, 21 Jun 2020 19:44:39: 7000000 INFO @ Sun, 21 Jun 2020 19:44:39: 2000000 INFO @ Sun, 21 Jun 2020 19:44:46: 8000000 INFO @ Sun, 21 Jun 2020 19:44:46: 3000000 INFO @ Sun, 21 Jun 2020 19:44:52: 9000000 INFO @ Sun, 21 Jun 2020 19:44:53: 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 19:44:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:55: #1 total tags in treatment: 9333692 INFO @ Sun, 21 Jun 2020 19:44:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:55: #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 19:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.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 19:44:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:55: #1 tags after filtering in treatment: 9333666 INFO @ Sun, 21 Jun 2020 19:44:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:56: #2 number of paired peaks: 205 WARNING @ Sun, 21 Jun 2020 19:44:56: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:56: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 19:44:56: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 19:44:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.05_model.r INFO @ Sun, 21 Jun 2020 19:44:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:59: 5000000 INFO @ Sun, 21 Jun 2020 19:45:02: 1000000 INFO @ Sun, 21 Jun 2020 19:45:06: 6000000 INFO @ Sun, 21 Jun 2020 19:45:09: 2000000 INFO @ Sun, 21 Jun 2020 19:45:13: 7000000 INFO @ Sun, 21 Jun 2020 19:45:16: 3000000 INFO @ Sun, 21 Jun 2020 19:45:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:20: 8000000 INFO @ Sun, 21 Jun 2020 19:45:22: 4000000 INFO @ Sun, 21 Jun 2020 19:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.05_summits.bed INFO @ Sun, 21 Jun 2020 19:45:27: Done! INFO @ Sun, 21 Jun 2020 19:45:27: 9000000 pass1 - making usageList (273 chroms): 1 millis pass2 - checking and writing primary data (3577 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:45:29: 5000000 INFO @ Sun, 21 Jun 2020 19:45:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:29: #1 total tags in treatment: 9333692 INFO @ Sun, 21 Jun 2020 19:45:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:29: #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 19:45:30: #1 tags after filtering in treatment: 9333666 INFO @ Sun, 21 Jun 2020 19:45:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:31: #2 number of paired peaks: 205 WARNING @ Sun, 21 Jun 2020 19:45:31: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 21 Jun 2020 19:45:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:31: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 19:45:31: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 19:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.10_model.r INFO @ Sun, 21 Jun 2020 19:45:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:36: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:45:42: 7000000 INFO @ Sun, 21 Jun 2020 19:45:48: 8000000 INFO @ Sun, 21 Jun 2020 19:45:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:54: 9000000 INFO @ Sun, 21 Jun 2020 19:45:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:56: #1 total tags in treatment: 9333692 INFO @ Sun, 21 Jun 2020 19:45:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:56: #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 19:45:57: #1 tags after filtering in treatment: 9333666 INFO @ Sun, 21 Jun 2020 19:45:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:57: #2 number of paired peaks: 205 WARNING @ Sun, 21 Jun 2020 19:45:57: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 21 Jun 2020 19:45:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:57: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 19:45:57: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 19:45:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.20_model.r INFO @ Sun, 21 Jun 2020 19:45:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:46:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.10_summits.bed INFO @ Sun, 21 Jun 2020 19:46:02: Done! BigWig に変換しました。 pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (1370 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:46:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:46:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331407/SRX331407.20_summits.bed INFO @ Sun, 21 Jun 2020 19:46:29: Done! pass1 - making usageList (65 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 3 millis CompletedMACS2peakCalling