Job ID = 6457075 SRX = SRX4375838 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:24:10 prefetch.2.10.7: 1) Downloading 'SRR7506492'... 2020-06-21T11:24:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:35 prefetch.2.10.7: 'SRR7506492' is valid 2020-06-21T11:25:35 prefetch.2.10.7: 1) 'SRR7506492' was downloaded successfully Read 5444932 spots for SRR7506492/SRR7506492.sra Written 5444932 spots for SRR7506492/SRR7506492.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: 00:01:09 5444932 reads; of these: 5444932 (100.00%) were unpaired; of these: 2157483 (39.62%) aligned 0 times 2477604 (45.50%) aligned exactly 1 time 809845 (14.87%) aligned >1 times 60.38% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 813239 / 3287449 = 0.2474 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 20:28:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.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 20:28:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:28:32: 1000000 INFO @ Sun, 21 Jun 2020 20:28:38: 2000000 INFO @ Sun, 21 Jun 2020 20:28:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:41: #1 total tags in treatment: 2474210 INFO @ Sun, 21 Jun 2020 20:28:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:41: #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 20:28:41: #1 tags after filtering in treatment: 2473870 INFO @ Sun, 21 Jun 2020 20:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:41: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:41: #2 number of paired peaks: 546 WARNING @ Sun, 21 Jun 2020 20:28:41: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:41: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 20:28:41: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 20:28:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.05_model.r INFO @ Sun, 21 Jun 2020 20:28:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.05_summits.bed INFO @ Sun, 21 Jun 2020 20:28:50: Done! pass1 - making usageList (240 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 20:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.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 20:28:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:02: 1000000 INFO @ Sun, 21 Jun 2020 20:29:08: 2000000 INFO @ Sun, 21 Jun 2020 20:29:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:11: #1 total tags in treatment: 2474210 INFO @ Sun, 21 Jun 2020 20:29:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:11: #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 20:29:11: #1 tags after filtering in treatment: 2473870 INFO @ Sun, 21 Jun 2020 20:29:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:12: #2 number of paired peaks: 546 WARNING @ Sun, 21 Jun 2020 20:29:12: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:12: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:12: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:12: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:12: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:12: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 20:29:12: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 20:29:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.10_model.r INFO @ Sun, 21 Jun 2020 20:29:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.10_summits.bed INFO @ Sun, 21 Jun 2020 20:29:21: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 20:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.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 20:29:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:32: 1000000 INFO @ Sun, 21 Jun 2020 20:29:38: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:29:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:41: #1 total tags in treatment: 2474210 INFO @ Sun, 21 Jun 2020 20:29:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:41: #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 20:29:42: #1 tags after filtering in treatment: 2473870 INFO @ Sun, 21 Jun 2020 20:29:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:42: #2 number of paired peaks: 546 WARNING @ Sun, 21 Jun 2020 20:29:42: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:42: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 20:29:42: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 20:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.20_model.r INFO @ Sun, 21 Jun 2020 20:29:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:29:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375838/SRX4375838.20_summits.bed INFO @ Sun, 21 Jun 2020 20:29:51: Done! pass1 - making usageList (39 chroms): 0 millis pass2 - checking and writing primary data (72 records, 4 fields): 2 millis CompletedMACS2peakCalling