Job ID = 6454833 SRX = SRX2592429 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:56 prefetch.2.10.7: 1) Downloading 'SRR5289706'... 2020-06-21T09:37:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:52 prefetch.2.10.7: 'SRR5289706' is valid 2020-06-21T09:39:52 prefetch.2.10.7: 1) 'SRR5289706' was downloaded successfully Read 11073917 spots for SRR5289706/SRR5289706.sra Written 11073917 spots for SRR5289706/SRR5289706.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: 00:03:39 11073917 reads; of these: 11073917 (100.00%) were unpaired; of these: 1545503 (13.96%) aligned 0 times 6697574 (60.48%) aligned exactly 1 time 2830840 (25.56%) aligned >1 times 86.04% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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_rmdupse_core] 3208809 / 9528414 = 0.3368 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 18:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.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 18:46:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:59: 1000000 INFO @ Sun, 21 Jun 2020 18:47:05: 2000000 INFO @ Sun, 21 Jun 2020 18:47:11: 3000000 INFO @ Sun, 21 Jun 2020 18:47:16: 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 18:47:23: 5000000 INFO @ Sun, 21 Jun 2020 18:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.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 18:47:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:28: 6000000 INFO @ Sun, 21 Jun 2020 18:47:30: 1000000 INFO @ Sun, 21 Jun 2020 18:47:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:31: #1 total tags in treatment: 6319605 INFO @ Sun, 21 Jun 2020 18:47:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:31: #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 18:47:31: #1 tags after filtering in treatment: 6319438 INFO @ Sun, 21 Jun 2020 18:47:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:32: #2 number of paired peaks: 416 WARNING @ Sun, 21 Jun 2020 18:47:32: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Sun, 21 Jun 2020 18:47:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:32: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 18:47:32: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 18:47:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.05_model.r INFO @ Sun, 21 Jun 2020 18:47:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:36: 2000000 INFO @ Sun, 21 Jun 2020 18:47:42: 3000000 INFO @ Sun, 21 Jun 2020 18:47:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:48: 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 18:47:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.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 18:47:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:54: 5000000 INFO @ Sun, 21 Jun 2020 18:47:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.05_summits.bed INFO @ Sun, 21 Jun 2020 18:47:55: Done! pass1 - making usageList (586 chroms): 3 millis pass2 - checking and writing primary data (14571 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:01: 1000000 INFO @ Sun, 21 Jun 2020 18:48:01: 6000000 INFO @ Sun, 21 Jun 2020 18:48:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:03: #1 total tags in treatment: 6319605 INFO @ Sun, 21 Jun 2020 18:48:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:03: #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 18:48:03: #1 tags after filtering in treatment: 6319438 INFO @ Sun, 21 Jun 2020 18:48:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:04: #2 number of paired peaks: 416 WARNING @ Sun, 21 Jun 2020 18:48:04: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Sun, 21 Jun 2020 18:48:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:04: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 18:48:04: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 18:48:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.10_model.r INFO @ Sun, 21 Jun 2020 18:48:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:08: 2000000 INFO @ Sun, 21 Jun 2020 18:48:16: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:48:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:23: 4000000 INFO @ Sun, 21 Jun 2020 18:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.10_summits.bed INFO @ Sun, 21 Jun 2020 18:48:28: Done! pass1 - making usageList (423 chroms): 2 millis pass2 - checking and writing primary data (11565 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:30: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:48:37: 6000000 INFO @ Sun, 21 Jun 2020 18:48:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:40: #1 total tags in treatment: 6319605 INFO @ Sun, 21 Jun 2020 18:48:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:40: #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 18:48:40: #1 tags after filtering in treatment: 6319438 INFO @ Sun, 21 Jun 2020 18:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:40: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:41: #2 number of paired peaks: 416 WARNING @ Sun, 21 Jun 2020 18:48:41: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Sun, 21 Jun 2020 18:48:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:41: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 18:48:41: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 18:48:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.20_model.r INFO @ Sun, 21 Jun 2020 18:48:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592429/SRX2592429.20_summits.bed INFO @ Sun, 21 Jun 2020 18:49:05: Done! pass1 - making usageList (246 chroms): 2 millis pass2 - checking and writing primary data (7960 records, 4 fields): 14 millis CompletedMACS2peakCalling