Job ID = 6456964 SRX = SRX4158196 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:47:51 prefetch.2.10.7: 1) Downloading 'SRR7253476'... 2020-06-21T11:47:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:49:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:49:30 prefetch.2.10.7: 'SRR7253476' is valid 2020-06-21T11:49:30 prefetch.2.10.7: 1) 'SRR7253476' was downloaded successfully Read 9555159 spots for SRR7253476/SRR7253476.sra Written 9555159 spots for SRR7253476/SRR7253476.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: 00:03:21 9555159 reads; of these: 9555159 (100.00%) were unpaired; of these: 686688 (7.19%) aligned 0 times 4646229 (48.63%) aligned exactly 1 time 4222242 (44.19%) aligned >1 times 92.81% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 1976047 / 8868471 = 0.2228 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 20:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.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 20:56:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:56:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:56:47: 1000000 INFO @ Sun, 21 Jun 2020 20:56:53: 2000000 INFO @ Sun, 21 Jun 2020 20:56:58: 3000000 INFO @ Sun, 21 Jun 2020 20:57:04: 4000000 INFO @ Sun, 21 Jun 2020 20:57:09: 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 20:57:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.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 20:57:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:15: 6000000 INFO @ Sun, 21 Jun 2020 20:57:17: 1000000 INFO @ Sun, 21 Jun 2020 20:57:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:57:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:57:21: #1 total tags in treatment: 6892424 INFO @ Sun, 21 Jun 2020 20:57:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:57:21: #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 20:57:21: #1 tags after filtering in treatment: 6892353 INFO @ Sun, 21 Jun 2020 20:57:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:57:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:57:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:57:22: #2 number of paired peaks: 1213 INFO @ Sun, 21 Jun 2020 20:57:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:57:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:57:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:57:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:57:22: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 20:57:22: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 20:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.05_model.r INFO @ Sun, 21 Jun 2020 20:57:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:57:22: 2000000 INFO @ Sun, 21 Jun 2020 20:57:28: 3000000 INFO @ Sun, 21 Jun 2020 20:57:33: 4000000 INFO @ Sun, 21 Jun 2020 20:57:38: 5000000 INFO @ Sun, 21 Jun 2020 20:57:39: #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 20:57:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.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 20:57:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:44: 6000000 INFO @ Sun, 21 Jun 2020 20:57:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:57:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:57:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.05_summits.bed INFO @ Sun, 21 Jun 2020 20:57:47: 1000000 INFO @ Sun, 21 Jun 2020 20:57:47: Done! pass1 - making usageList (703 chroms): 2 millis pass2 - checking and writing primary data (3331 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:57:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:57:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:57:49: #1 total tags in treatment: 6892424 INFO @ Sun, 21 Jun 2020 20:57:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:57:49: #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 20:57:50: #1 tags after filtering in treatment: 6892353 INFO @ Sun, 21 Jun 2020 20:57:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:57:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:57:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:57:51: #2 number of paired peaks: 1213 INFO @ Sun, 21 Jun 2020 20:57:51: start model_add_line... INFO @ Sun, 21 Jun 2020 20:57:51: start X-correlation... INFO @ Sun, 21 Jun 2020 20:57:51: end of X-cor INFO @ Sun, 21 Jun 2020 20:57:51: #2 finished! INFO @ Sun, 21 Jun 2020 20:57:51: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 20:57:51: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 20:57:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.10_model.r INFO @ Sun, 21 Jun 2020 20:57:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:57:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:57:53: 2000000 INFO @ Sun, 21 Jun 2020 20:57:58: 3000000 INFO @ Sun, 21 Jun 2020 20:58:04: 4000000 INFO @ Sun, 21 Jun 2020 20:58:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:58:09: 5000000 INFO @ Sun, 21 Jun 2020 20:58:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.10_summits.bed INFO @ Sun, 21 Jun 2020 20:58:15: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (1235 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:58:15: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:58:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:58:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:58:21: #1 total tags in treatment: 6892424 INFO @ Sun, 21 Jun 2020 20:58:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:21: #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 20:58:21: #1 tags after filtering in treatment: 6892353 INFO @ Sun, 21 Jun 2020 20:58:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:58:22: #2 number of paired peaks: 1213 INFO @ Sun, 21 Jun 2020 20:58:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:22: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 20:58:22: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 20:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.20_model.r INFO @ Sun, 21 Jun 2020 20:58:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:58:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158196/SRX4158196.20_summits.bed INFO @ Sun, 21 Jun 2020 20:58:47: Done! pass1 - making usageList (241 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 14 millis CompletedMACS2peakCalling