Job ID = 6453928 SRX = SRX160145 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:55:19 prefetch.2.10.7: 1) Downloading 'SRR522007'... 2020-06-21T08:55:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:58:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:58:38 prefetch.2.10.7: 'SRR522007' is valid 2020-06-21T08:58:38 prefetch.2.10.7: 1) 'SRR522007' was downloaded successfully Read 18529623 spots for SRR522007/SRR522007.sra Written 18529623 spots for SRR522007/SRR522007.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: 00:07:58 18529623 reads; of these: 18529623 (100.00%) were unpaired; of these: 968988 (5.23%) aligned 0 times 7848191 (42.35%) aligned exactly 1 time 9712444 (52.42%) aligned >1 times 94.77% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 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 8 files... [bam_rmdupse_core] 14612151 / 17560635 = 0.8321 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 18:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.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 18:10:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:24: 1000000 INFO @ Sun, 21 Jun 2020 18:10:29: 2000000 INFO @ Sun, 21 Jun 2020 18:10:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:10:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:10:34: #1 total tags in treatment: 2948484 INFO @ Sun, 21 Jun 2020 18:10:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:34: #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 18:10:34: #1 tags after filtering in treatment: 2948367 INFO @ Sun, 21 Jun 2020 18:10:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:34: #2 number of paired peaks: 5016 INFO @ Sun, 21 Jun 2020 18:10:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:34: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 18:10:34: #2 alternative fragment length(s) may be 4,218 bps INFO @ Sun, 21 Jun 2020 18:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.05_model.r INFO @ Sun, 21 Jun 2020 18:10:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.05_summits.bed INFO @ Sun, 21 Jun 2020 18:10:46: Done! pass1 - making usageList (802 chroms): 2 millis pass2 - checking and writing primary data (2591 records, 4 fields): 21 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 18:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.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 18:10:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:54: 1000000 INFO @ Sun, 21 Jun 2020 18:10:59: 2000000 INFO @ Sun, 21 Jun 2020 18:11:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:11:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:11:04: #1 total tags in treatment: 2948484 INFO @ Sun, 21 Jun 2020 18:11:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:04: #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 18:11:05: #1 tags after filtering in treatment: 2948367 INFO @ Sun, 21 Jun 2020 18:11:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:05: #2 number of paired peaks: 5016 INFO @ Sun, 21 Jun 2020 18:11:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:05: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 18:11:05: #2 alternative fragment length(s) may be 4,218 bps INFO @ Sun, 21 Jun 2020 18:11:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.10_model.r INFO @ Sun, 21 Jun 2020 18:11:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:11:14: #3 Call peaks for each chromosome... 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 18:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.10_summits.bed INFO @ Sun, 21 Jun 2020 18:11:18: Done! pass1 - making usageList (656 chroms): 1 millis pass2 - checking and writing primary data (1529 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.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 18:11:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:24: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:11:29: 2000000 INFO @ Sun, 21 Jun 2020 18:11:35: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:11:35: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:11:35: #1 total tags in treatment: 2948484 INFO @ Sun, 21 Jun 2020 18:11:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:35: #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 18:11:35: #1 tags after filtering in treatment: 2948367 INFO @ Sun, 21 Jun 2020 18:11:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:35: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:11:36: #2 number of paired peaks: 5016 INFO @ Sun, 21 Jun 2020 18:11:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:36: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 18:11:36: #2 alternative fragment length(s) may be 4,218 bps INFO @ Sun, 21 Jun 2020 18:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.20_model.r INFO @ Sun, 21 Jun 2020 18:11:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:11:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX160145/SRX160145.20_summits.bed INFO @ Sun, 21 Jun 2020 18:11:49: Done! pass1 - making usageList (285 chroms): 1 millis pass2 - checking and writing primary data (579 records, 4 fields): 9 millis CompletedMACS2peakCalling