Job ID = 6454694 SRX = SRX2520643 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:28:44 prefetch.2.10.7: 1) Downloading 'SRR5206762'... 2020-06-21T09:28:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:30:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:31:00 prefetch.2.10.7: 'SRR5206762' is valid 2020-06-21T09:31:00 prefetch.2.10.7: 1) 'SRR5206762' was downloaded successfully Read 22861352 spots for SRR5206762/SRR5206762.sra Written 22861352 spots for SRR5206762/SRR5206762.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: 00:05:56 22861352 reads; of these: 22861352 (100.00%) were unpaired; of these: 1499725 (6.56%) aligned 0 times 16869737 (73.79%) aligned exactly 1 time 4491890 (19.65%) aligned >1 times 93.44% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 2554813 / 21361627 = 0.1196 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 18:42:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.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 18:42:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:35: 1000000 INFO @ Sun, 21 Jun 2020 18:42:40: 2000000 INFO @ Sun, 21 Jun 2020 18:42:45: 3000000 INFO @ Sun, 21 Jun 2020 18:42:50: 4000000 INFO @ Sun, 21 Jun 2020 18:42:55: 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 18:42:59: 6000000 INFO @ Sun, 21 Jun 2020 18:43:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.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 18:43:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:05: 7000000 INFO @ Sun, 21 Jun 2020 18:43:06: 1000000 INFO @ Sun, 21 Jun 2020 18:43:10: 8000000 INFO @ Sun, 21 Jun 2020 18:43:12: 2000000 INFO @ Sun, 21 Jun 2020 18:43:15: 9000000 INFO @ Sun, 21 Jun 2020 18:43:18: 3000000 INFO @ Sun, 21 Jun 2020 18:43:20: 10000000 INFO @ Sun, 21 Jun 2020 18:43:24: 4000000 INFO @ Sun, 21 Jun 2020 18:43:26: 11000000 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 18:43:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.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 18:43:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:30: 5000000 INFO @ Sun, 21 Jun 2020 18:43:31: 12000000 INFO @ Sun, 21 Jun 2020 18:43:36: 13000000 INFO @ Sun, 21 Jun 2020 18:43:36: 1000000 INFO @ Sun, 21 Jun 2020 18:43:36: 6000000 INFO @ Sun, 21 Jun 2020 18:43:41: 14000000 INFO @ Sun, 21 Jun 2020 18:43:43: 2000000 INFO @ Sun, 21 Jun 2020 18:43:43: 7000000 INFO @ Sun, 21 Jun 2020 18:43:47: 15000000 INFO @ Sun, 21 Jun 2020 18:43:49: 3000000 INFO @ Sun, 21 Jun 2020 18:43:49: 8000000 INFO @ Sun, 21 Jun 2020 18:43:53: 16000000 INFO @ Sun, 21 Jun 2020 18:43:55: 9000000 INFO @ Sun, 21 Jun 2020 18:43:55: 4000000 INFO @ Sun, 21 Jun 2020 18:43:58: 17000000 INFO @ Sun, 21 Jun 2020 18:44:01: 10000000 INFO @ Sun, 21 Jun 2020 18:44:01: 5000000 INFO @ Sun, 21 Jun 2020 18:44:04: 18000000 INFO @ Sun, 21 Jun 2020 18:44:07: 11000000 INFO @ Sun, 21 Jun 2020 18:44:07: 6000000 INFO @ Sun, 21 Jun 2020 18:44:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:44:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:44:08: #1 total tags in treatment: 18806814 INFO @ Sun, 21 Jun 2020 18:44:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:08: #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 18:44:09: #1 tags after filtering in treatment: 18806740 INFO @ Sun, 21 Jun 2020 18:44:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:10: #2 number of paired peaks: 596 WARNING @ Sun, 21 Jun 2020 18:44:10: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Sun, 21 Jun 2020 18:44:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:10: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 18:44:10: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 18:44:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.05_model.r INFO @ Sun, 21 Jun 2020 18:44:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:13: 12000000 INFO @ Sun, 21 Jun 2020 18:44:14: 7000000 INFO @ Sun, 21 Jun 2020 18:44:19: 13000000 INFO @ Sun, 21 Jun 2020 18:44:20: 8000000 INFO @ Sun, 21 Jun 2020 18:44:25: 14000000 INFO @ Sun, 21 Jun 2020 18:44:26: 9000000 INFO @ Sun, 21 Jun 2020 18:44:31: 15000000 INFO @ Sun, 21 Jun 2020 18:44:31: 10000000 INFO @ Sun, 21 Jun 2020 18:44:37: 11000000 INFO @ Sun, 21 Jun 2020 18:44:37: 16000000 INFO @ Sun, 21 Jun 2020 18:44:43: 12000000 INFO @ Sun, 21 Jun 2020 18:44:44: 17000000 INFO @ Sun, 21 Jun 2020 18:44:49: 13000000 INFO @ Sun, 21 Jun 2020 18:44:50: 18000000 INFO @ Sun, 21 Jun 2020 18:44:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:44:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:44:55: #1 total tags in treatment: 18806814 INFO @ Sun, 21 Jun 2020 18:44:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:55: #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 18:44:55: 14000000 INFO @ Sun, 21 Jun 2020 18:44:55: #1 tags after filtering in treatment: 18806740 INFO @ Sun, 21 Jun 2020 18:44:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:57: #2 number of paired peaks: 596 WARNING @ Sun, 21 Jun 2020 18:44:57: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Sun, 21 Jun 2020 18:44:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:57: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 18:44:57: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 18:44:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.10_model.r INFO @ Sun, 21 Jun 2020 18:44:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:01: 15000000 INFO @ Sun, 21 Jun 2020 18:45:07: 16000000 INFO @ Sun, 21 Jun 2020 18:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:10: Done! pass1 - making usageList (374 chroms): 2 millis pass2 - checking and writing primary data (6564 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:13: 17000000 INFO @ Sun, 21 Jun 2020 18:45:18: 18000000 INFO @ Sun, 21 Jun 2020 18:45:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:45:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:45:23: #1 total tags in treatment: 18806814 INFO @ Sun, 21 Jun 2020 18:45:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:23: #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 18:45:24: #1 tags after filtering in treatment: 18806740 INFO @ Sun, 21 Jun 2020 18:45:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:25: #2 number of paired peaks: 596 WARNING @ Sun, 21 Jun 2020 18:45:25: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:25: #2 predicted fragment length is 137 bps INFO @ Sun, 21 Jun 2020 18:45:25: #2 alternative fragment length(s) may be 137 bps INFO @ Sun, 21 Jun 2020 18:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.20_model.r INFO @ Sun, 21 Jun 2020 18:45:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:45:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.10_summits.bed INFO @ Sun, 21 Jun 2020 18:45:58: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (3111 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520643/SRX2520643.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:25: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (1034 records, 4 fields): 8 millis CompletedMACS2peakCalling