Job ID = 6457110 SRX = SRX4375867 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 'SRR7506521'... 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: 'SRR7506521' is valid 2020-06-21T11:25:35 prefetch.2.10.7: 1) 'SRR7506521' was downloaded successfully Read 5210854 spots for SRR7506521/SRR7506521.sra Written 5210854 spots for SRR7506521/SRR7506521.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: 00:01:40 5210854 reads; of these: 5210854 (100.00%) were unpaired; of these: 1468769 (28.19%) aligned 0 times 2490981 (47.80%) aligned exactly 1 time 1251104 (24.01%) aligned >1 times 71.81% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 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] 1286861 / 3742085 = 0.3439 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 20:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.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 20:28:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:28:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:02: 1000000 INFO @ Sun, 21 Jun 2020 20:29:09: 2000000 INFO @ Sun, 21 Jun 2020 20:29:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:12: #1 total tags in treatment: 2455224 INFO @ Sun, 21 Jun 2020 20:29:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:12: #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 20:29:13: #1 tags after filtering in treatment: 2454954 INFO @ Sun, 21 Jun 2020 20:29:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:13: #2 number of paired peaks: 969 WARNING @ Sun, 21 Jun 2020 20:29:13: Fewer paired peaks (969) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 969 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:13: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:29:13: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 20:29:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.05_model.r INFO @ Sun, 21 Jun 2020 20:29:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.05_summits.bed INFO @ Sun, 21 Jun 2020 20:29:22: Done! pass1 - making usageList (522 chroms): 1 millis pass2 - checking and writing primary data (1494 records, 4 fields): 16 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 20:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.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 20:29:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:32: 1000000 INFO @ Sun, 21 Jun 2020 20:29:39: 2000000 INFO @ Sun, 21 Jun 2020 20:29:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:43: #1 total tags in treatment: 2455224 INFO @ Sun, 21 Jun 2020 20:29:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:43: #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 20:29:43: #1 tags after filtering in treatment: 2454954 INFO @ Sun, 21 Jun 2020 20:29:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:43: #2 number of paired peaks: 969 WARNING @ Sun, 21 Jun 2020 20:29:43: Fewer paired peaks (969) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 969 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:43: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:29:43: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 20:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.10_model.r INFO @ Sun, 21 Jun 2020 20:29:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.10_summits.bed INFO @ Sun, 21 Jun 2020 20:29:52: Done! pass1 - making usageList (335 chroms): 1 millis pass2 - checking and writing primary data (642 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 20:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.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 20:29:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:02: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:30:09: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:30:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:30:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:30:13: #1 total tags in treatment: 2455224 INFO @ Sun, 21 Jun 2020 20:30:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:30:13: #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 20:30:13: #1 tags after filtering in treatment: 2454954 INFO @ Sun, 21 Jun 2020 20:30:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:30:13: #2 number of paired peaks: 969 WARNING @ Sun, 21 Jun 2020 20:30:13: Fewer paired peaks (969) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 969 pairs to build model! INFO @ Sun, 21 Jun 2020 20:30:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:30:13: start X-correlation... INFO @ Sun, 21 Jun 2020 20:30:13: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:13: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:13: #2 predicted fragment length is 104 bps INFO @ Sun, 21 Jun 2020 20:30:13: #2 alternative fragment length(s) may be 104 bps INFO @ Sun, 21 Jun 2020 20:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.20_model.r INFO @ Sun, 21 Jun 2020 20:30:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:30:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375867/SRX4375867.20_summits.bed INFO @ Sun, 21 Jun 2020 20:30:21: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 3 millis CompletedMACS2peakCalling