Job ID = 6454813 SRX = SRX2592412 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:45:10 prefetch.2.10.7: 1) Downloading 'SRR5289689'... 2020-06-21T09:45:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:49:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:49:04 prefetch.2.10.7: 1) 'SRR5289689' was downloaded successfully Read 24742813 spots for SRR5289689/SRR5289689.sra Written 24742813 spots for SRR5289689/SRR5289689.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: 00:07:33 24742813 reads; of these: 24742813 (100.00%) were unpaired; of these: 1890210 (7.64%) aligned 0 times 18226918 (73.67%) aligned exactly 1 time 4625685 (18.70%) aligned >1 times 92.36% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 8132959 / 22852603 = 0.3559 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 19:03:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.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 19:03:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:47: 1000000 INFO @ Sun, 21 Jun 2020 19:03:53: 2000000 INFO @ Sun, 21 Jun 2020 19:03:58: 3000000 INFO @ Sun, 21 Jun 2020 19:04:03: 4000000 INFO @ Sun, 21 Jun 2020 19:04:09: 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 19:04:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.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 19:04:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:14: 6000000 INFO @ Sun, 21 Jun 2020 19:04:17: 1000000 INFO @ Sun, 21 Jun 2020 19:04:20: 7000000 INFO @ Sun, 21 Jun 2020 19:04:23: 2000000 INFO @ Sun, 21 Jun 2020 19:04:26: 8000000 INFO @ Sun, 21 Jun 2020 19:04:28: 3000000 INFO @ Sun, 21 Jun 2020 19:04:31: 9000000 INFO @ Sun, 21 Jun 2020 19:04:34: 4000000 INFO @ Sun, 21 Jun 2020 19:04:37: 10000000 INFO @ Sun, 21 Jun 2020 19:04:39: 5000000 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 19:04:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.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 19:04:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:42: 11000000 INFO @ Sun, 21 Jun 2020 19:04:45: 6000000 INFO @ Sun, 21 Jun 2020 19:04:48: 1000000 INFO @ Sun, 21 Jun 2020 19:04:49: 12000000 INFO @ Sun, 21 Jun 2020 19:04:51: 7000000 INFO @ Sun, 21 Jun 2020 19:04:53: 2000000 INFO @ Sun, 21 Jun 2020 19:04:54: 13000000 INFO @ Sun, 21 Jun 2020 19:04:56: 8000000 INFO @ Sun, 21 Jun 2020 19:04:59: 3000000 INFO @ Sun, 21 Jun 2020 19:05:00: 14000000 INFO @ Sun, 21 Jun 2020 19:05:02: 9000000 INFO @ Sun, 21 Jun 2020 19:05:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:04: #1 total tags in treatment: 14719644 INFO @ Sun, 21 Jun 2020 19:05:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:04: #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 19:05:05: #1 tags after filtering in treatment: 14719549 INFO @ Sun, 21 Jun 2020 19:05:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:05: 4000000 INFO @ Sun, 21 Jun 2020 19:05:06: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 19:05:06: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:06: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:05:06: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sun, 21 Jun 2020 19:05:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.05_model.r INFO @ Sun, 21 Jun 2020 19:05:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:08: 10000000 INFO @ Sun, 21 Jun 2020 19:05:11: 5000000 INFO @ Sun, 21 Jun 2020 19:05:13: 11000000 INFO @ Sun, 21 Jun 2020 19:05:16: 6000000 INFO @ Sun, 21 Jun 2020 19:05:19: 12000000 INFO @ Sun, 21 Jun 2020 19:05:22: 7000000 INFO @ Sun, 21 Jun 2020 19:05:25: 13000000 INFO @ Sun, 21 Jun 2020 19:05:28: 8000000 INFO @ Sun, 21 Jun 2020 19:05:30: 14000000 INFO @ Sun, 21 Jun 2020 19:05:33: 9000000 INFO @ Sun, 21 Jun 2020 19:05:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:34: #1 total tags in treatment: 14719644 INFO @ Sun, 21 Jun 2020 19:05:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:34: #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 19:05:35: #1 tags after filtering in treatment: 14719549 INFO @ Sun, 21 Jun 2020 19:05:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:36: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 19:05:36: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:36: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:05:36: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sun, 21 Jun 2020 19:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.10_model.r INFO @ Sun, 21 Jun 2020 19:05:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:39: 10000000 INFO @ Sun, 21 Jun 2020 19:05:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:44: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:05:50: 12000000 INFO @ Sun, 21 Jun 2020 19:05:56: 13000000 INFO @ Sun, 21 Jun 2020 19:06:01: 14000000 INFO @ Sun, 21 Jun 2020 19:06:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.05_summits.bed INFO @ Sun, 21 Jun 2020 19:06:04: Done! pass1 - making usageList (253 chroms): 3 millis pass2 - checking and writing primary data (17418 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:06:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:05: #1 total tags in treatment: 14719644 INFO @ Sun, 21 Jun 2020 19:06:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:05: #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 19:06:06: #1 tags after filtering in treatment: 14719549 INFO @ Sun, 21 Jun 2020 19:06:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:07: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 19:06:07: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 19:06:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:07: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 19:06:07: #2 alternative fragment length(s) may be 4,169 bps INFO @ Sun, 21 Jun 2020 19:06:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.20_model.r INFO @ Sun, 21 Jun 2020 19:06:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:06:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.10_summits.bed INFO @ Sun, 21 Jun 2020 19:06:33: Done! pass1 - making usageList (186 chroms): 2 millis pass2 - checking and writing primary data (12454 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:06:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592412/SRX2592412.20_summits.bed INFO @ Sun, 21 Jun 2020 19:07:05: Done! pass1 - making usageList (132 chroms): 2 millis pass2 - checking and writing primary data (7426 records, 4 fields): 13 millis CompletedMACS2peakCalling