Job ID = 6452386 SRX = SRX013025 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:31:04 prefetch.2.10.7: 1) Downloading 'SRR030291'... 2020-06-21T07:31:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:22 prefetch.2.10.7: 'SRR030291' is valid 2020-06-21T07:32:22 prefetch.2.10.7: 1) 'SRR030291' was downloaded successfully Read 6986464 spots for SRR030291/SRR030291.sra Written 6986464 spots for SRR030291/SRR030291.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: 00:01:08 6986464 reads; of these: 6986464 (100.00%) were unpaired; of these: 192553 (2.76%) aligned 0 times 6228137 (89.15%) aligned exactly 1 time 565774 (8.10%) aligned >1 times 97.24% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 463810 / 6793911 = 0.0683 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 16:35:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.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 16:35:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:35:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:35:36: 1000000 INFO @ Sun, 21 Jun 2020 16:35:43: 2000000 INFO @ Sun, 21 Jun 2020 16:35:49: 3000000 INFO @ Sun, 21 Jun 2020 16:35:56: 4000000 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 16:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.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 16:36:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:36:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:36:02: 5000000 INFO @ Sun, 21 Jun 2020 16:36:07: 1000000 INFO @ Sun, 21 Jun 2020 16:36:09: 6000000 INFO @ Sun, 21 Jun 2020 16:36:11: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:36:11: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:36:11: #1 total tags in treatment: 6330101 INFO @ Sun, 21 Jun 2020 16:36:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:11: #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 16:36:12: #1 tags after filtering in treatment: 6329884 INFO @ Sun, 21 Jun 2020 16:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:12: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:12: #2 number of paired peaks: 2028 INFO @ Sun, 21 Jun 2020 16:36:12: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:12: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:12: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:12: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:12: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 16:36:12: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 16:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.05_model.r INFO @ Sun, 21 Jun 2020 16:36:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:36:13: 2000000 INFO @ Sun, 21 Jun 2020 16:36:20: 3000000 INFO @ Sun, 21 Jun 2020 16:36:26: 4000000 INFO @ Sun, 21 Jun 2020 16:36:27: #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 16:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.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 16:36:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:36:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:36:32: 5000000 INFO @ Sun, 21 Jun 2020 16:36:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:36:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:36:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.05_summits.bed INFO @ Sun, 21 Jun 2020 16:36:35: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (8858 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:36:37: 1000000 INFO @ Sun, 21 Jun 2020 16:36:39: 6000000 INFO @ Sun, 21 Jun 2020 16:36:41: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:36:41: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:36:41: #1 total tags in treatment: 6330101 INFO @ Sun, 21 Jun 2020 16:36:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:36:41: #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 16:36:42: #1 tags after filtering in treatment: 6329884 INFO @ Sun, 21 Jun 2020 16:36:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:36:42: #1 finished! INFO @ Sun, 21 Jun 2020 16:36:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:36:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:36:42: #2 number of paired peaks: 2028 INFO @ Sun, 21 Jun 2020 16:36:42: start model_add_line... INFO @ Sun, 21 Jun 2020 16:36:42: start X-correlation... INFO @ Sun, 21 Jun 2020 16:36:42: end of X-cor INFO @ Sun, 21 Jun 2020 16:36:42: #2 finished! INFO @ Sun, 21 Jun 2020 16:36:42: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 16:36:42: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 16:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.10_model.r INFO @ Sun, 21 Jun 2020 16:36:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:36:44: 2000000 INFO @ Sun, 21 Jun 2020 16:36:51: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:36:57: 4000000 INFO @ Sun, 21 Jun 2020 16:36:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:37:04: 5000000 INFO @ Sun, 21 Jun 2020 16:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.10_summits.bed INFO @ Sun, 21 Jun 2020 16:37:05: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (4167 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:37:10: 6000000 INFO @ Sun, 21 Jun 2020 16:37:13: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:37:13: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:37:13: #1 total tags in treatment: 6330101 INFO @ Sun, 21 Jun 2020 16:37:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:37:13: #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 16:37:13: #1 tags after filtering in treatment: 6329884 INFO @ Sun, 21 Jun 2020 16:37:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:37:13: #1 finished! INFO @ Sun, 21 Jun 2020 16:37:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:37:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:37:13: #2 number of paired peaks: 2028 INFO @ Sun, 21 Jun 2020 16:37:13: start model_add_line... INFO @ Sun, 21 Jun 2020 16:37:14: start X-correlation... INFO @ Sun, 21 Jun 2020 16:37:14: end of X-cor INFO @ Sun, 21 Jun 2020 16:37:14: #2 finished! INFO @ Sun, 21 Jun 2020 16:37:14: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 16:37:14: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 21 Jun 2020 16:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.20_model.r INFO @ Sun, 21 Jun 2020 16:37:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:37:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:37:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:37:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:37:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013025/SRX013025.20_summits.bed INFO @ Sun, 21 Jun 2020 16:37:36: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 3 millis CompletedMACS2peakCalling