Job ID = 6457111 SRX = SRX4375868 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:30:10 prefetch.2.10.7: 1) Downloading 'SRR7506522'... 2020-06-21T11:30:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:31:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:31:16 prefetch.2.10.7: 'SRR7506522' is valid 2020-06-21T11:31:16 prefetch.2.10.7: 1) 'SRR7506522' was downloaded successfully Read 4544490 spots for SRR7506522/SRR7506522.sra Written 4544490 spots for SRR7506522/SRR7506522.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: 00:01:14 4544490 reads; of these: 4544490 (100.00%) were unpaired; of these: 1500733 (33.02%) aligned 0 times 2138928 (47.07%) aligned exactly 1 time 904829 (19.91%) aligned >1 times 66.98% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 793534 / 3043757 = 0.2607 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 20:34:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.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 20:34:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:09: 1000000 INFO @ Sun, 21 Jun 2020 20:34:15: 2000000 INFO @ Sun, 21 Jun 2020 20:34:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:34:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:34:17: #1 total tags in treatment: 2250223 INFO @ Sun, 21 Jun 2020 20:34:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:17: #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 20:34:17: #1 tags after filtering in treatment: 2249935 INFO @ Sun, 21 Jun 2020 20:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:18: #2 number of paired peaks: 946 WARNING @ Sun, 21 Jun 2020 20:34:18: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:18: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:18: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:18: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:18: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:18: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 20:34:18: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 20:34:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.05_model.r INFO @ Sun, 21 Jun 2020 20:34:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.05_summits.bed INFO @ Sun, 21 Jun 2020 20:34:26: Done! pass1 - making usageList (494 chroms): 2 millis pass2 - checking and writing primary data (1266 records, 4 fields): 14 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 20:34:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.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 20:34:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:39: 1000000 INFO @ Sun, 21 Jun 2020 20:34:45: 2000000 INFO @ Sun, 21 Jun 2020 20:34:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:34:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:34:47: #1 total tags in treatment: 2250223 INFO @ Sun, 21 Jun 2020 20:34:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:47: #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 20:34:47: #1 tags after filtering in treatment: 2249935 INFO @ Sun, 21 Jun 2020 20:34:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:47: #2 number of paired peaks: 946 WARNING @ Sun, 21 Jun 2020 20:34:47: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:47: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:47: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:47: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:47: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 20:34:47: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 20:34:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.10_model.r INFO @ Sun, 21 Jun 2020 20:34:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.10_summits.bed INFO @ Sun, 21 Jun 2020 20:34:56: Done! pass1 - making usageList (308 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 9 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 20:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.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 20:35:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:35:16: 2000000 INFO @ Sun, 21 Jun 2020 20:35:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:35:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:35:17: #1 total tags in treatment: 2250223 INFO @ Sun, 21 Jun 2020 20:35:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:35:17: #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 20:35:18: #1 tags after filtering in treatment: 2249935 INFO @ Sun, 21 Jun 2020 20:35:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:35:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:35:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:35:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:35:18: #2 number of paired peaks: 946 WARNING @ Sun, 21 Jun 2020 20:35:18: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Sun, 21 Jun 2020 20:35:18: start model_add_line... INFO @ Sun, 21 Jun 2020 20:35:18: start X-correlation... INFO @ Sun, 21 Jun 2020 20:35:18: end of X-cor INFO @ Sun, 21 Jun 2020 20:35:18: #2 finished! INFO @ Sun, 21 Jun 2020 20:35:18: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 20:35:18: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 20:35:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.20_model.r INFO @ Sun, 21 Jun 2020 20:35:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:35:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:35:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375868/SRX4375868.20_summits.bed INFO @ Sun, 21 Jun 2020 20:35:27: Done! pass1 - making usageList (94 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 3 millis CompletedMACS2peakCalling