Job ID = 6457264 SRX = SRX4639144 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:42:25 prefetch.2.10.7: 1) Downloading 'SRR7784125'... 2020-06-21T11:42:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:15 prefetch.2.10.7: 'SRR7784125' is valid 2020-06-21T11:45:15 prefetch.2.10.7: 1) 'SRR7784125' was downloaded successfully Read 13107189 spots for SRR7784125/SRR7784125.sra Written 13107189 spots for SRR7784125/SRR7784125.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: 00:02:38 13107189 reads; of these: 13107189 (100.00%) were unpaired; of these: 5737268 (43.77%) aligned 0 times 5462153 (41.67%) aligned exactly 1 time 1907768 (14.56%) aligned >1 times 56.23% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 2432073 / 7369921 = 0.3300 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 20:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.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 20:50:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:43: 1000000 INFO @ Sun, 21 Jun 2020 20:50:49: 2000000 INFO @ Sun, 21 Jun 2020 20:50:54: 3000000 INFO @ Sun, 21 Jun 2020 20:50:59: 4000000 INFO @ Sun, 21 Jun 2020 20:51:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:51:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:51:04: #1 total tags in treatment: 4937848 INFO @ Sun, 21 Jun 2020 20:51:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:04: #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 20:51:05: #1 tags after filtering in treatment: 4937792 INFO @ Sun, 21 Jun 2020 20:51:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:05: #2 number of paired peaks: 1344 INFO @ Sun, 21 Jun 2020 20:51:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:05: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 20:51:05: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 20:51:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.05_model.r INFO @ Sun, 21 Jun 2020 20:51:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:05: #3 Pre-compute pvalue-qvalue table... 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 20:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.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 20:51:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:14: 1000000 INFO @ Sun, 21 Jun 2020 20:51:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:20: 2000000 INFO @ Sun, 21 Jun 2020 20:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.05_summits.bed INFO @ Sun, 21 Jun 2020 20:51:22: Done! pass1 - making usageList (602 chroms): 1 millis pass2 - checking and writing primary data (2124 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:51:26: 3000000 INFO @ Sun, 21 Jun 2020 20:51:33: 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 20:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.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 20:51:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:51:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:51:39: #1 total tags in treatment: 4937848 INFO @ Sun, 21 Jun 2020 20:51:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:39: #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 20:51:39: #1 tags after filtering in treatment: 4937792 INFO @ Sun, 21 Jun 2020 20:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:39: #2 number of paired peaks: 1344 INFO @ Sun, 21 Jun 2020 20:51:39: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:39: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:39: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:39: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:39: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 20:51:39: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 20:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.10_model.r INFO @ Sun, 21 Jun 2020 20:51:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:44: 1000000 INFO @ Sun, 21 Jun 2020 20:51:50: 2000000 INFO @ Sun, 21 Jun 2020 20:51:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.10_summits.bed INFO @ Sun, 21 Jun 2020 20:51:56: Done! pass1 - making usageList (534 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:51:57: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:52:03: 4000000 INFO @ Sun, 21 Jun 2020 20:52:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:52:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:52:09: #1 total tags in treatment: 4937848 INFO @ Sun, 21 Jun 2020 20:52:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:09: #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 20:52:09: #1 tags after filtering in treatment: 4937792 INFO @ Sun, 21 Jun 2020 20:52:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:09: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:10: #2 number of paired peaks: 1344 INFO @ Sun, 21 Jun 2020 20:52:10: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:10: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:10: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:10: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:10: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 20:52:10: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 20:52:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.20_model.r INFO @ Sun, 21 Jun 2020 20:52:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:52:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4639144/SRX4639144.20_summits.bed INFO @ Sun, 21 Jun 2020 20:52:27: Done! pass1 - making usageList (399 chroms): 1 millis pass2 - checking and writing primary data (784 records, 4 fields): 11 millis CompletedMACS2peakCalling