Job ID = 6497328 SRX = SRX1010106 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:17:19 prefetch.2.10.7: 1) Downloading 'SRR1998062'... 2020-06-25T21:17:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:18:06 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:18:07 prefetch.2.10.7: 'SRR1998062' is valid 2020-06-25T21:18:07 prefetch.2.10.7: 1) 'SRR1998062' was downloaded successfully Read 1846797 spots for SRR1998062/SRR1998062.sra Written 1846797 spots for SRR1998062/SRR1998062.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: 00:00:01 Multiseed full-index search: 00:02:40 1846797 reads; of these: 1846797 (100.00%) were paired; of these: 1012162 (54.81%) aligned concordantly 0 times 576794 (31.23%) aligned concordantly exactly 1 time 257841 (13.96%) aligned concordantly >1 times ---- 1012162 pairs aligned concordantly 0 times; of these: 137129 (13.55%) aligned discordantly 1 time ---- 875033 pairs aligned 0 times concordantly or discordantly; of these: 1750066 mates make up the pairs; of these: 1047567 (59.86%) aligned 0 times 274581 (15.69%) aligned exactly 1 time 427918 (24.45%) aligned >1 times 71.64% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 329940 / 880575 = 0.3747 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 @ Fri, 26 Jun 2020 06:22:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 26 Jun 2020 06:22:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:22:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:22:15: 1000000 INFO @ Fri, 26 Jun 2020 06:22:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:22:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:22:21: #1 total tags in treatment: 521295 INFO @ Fri, 26 Jun 2020 06:22:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:22:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:22:21: #1 tags after filtering in treatment: 458533 INFO @ Fri, 26 Jun 2020 06:22:21: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 06:22:21: #1 finished! INFO @ Fri, 26 Jun 2020 06:22:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:22:21: #2 number of paired peaks: 1825 INFO @ Fri, 26 Jun 2020 06:22:21: start model_add_line... INFO @ Fri, 26 Jun 2020 06:22:21: start X-correlation... INFO @ Fri, 26 Jun 2020 06:22:21: end of X-cor INFO @ Fri, 26 Jun 2020 06:22:21: #2 finished! INFO @ Fri, 26 Jun 2020 06:22:21: #2 predicted fragment length is 237 bps INFO @ Fri, 26 Jun 2020 06:22:21: #2 alternative fragment length(s) may be 237 bps INFO @ Fri, 26 Jun 2020 06:22:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.05_model.r INFO @ Fri, 26 Jun 2020 06:22:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:22:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:22:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.05_summits.bed INFO @ Fri, 26 Jun 2020 06:22:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1274 records, 4 fields): 3 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 @ Fri, 26 Jun 2020 06:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 26 Jun 2020 06:22:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:22:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:22:45: 1000000 INFO @ Fri, 26 Jun 2020 06:22:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:22:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:22:51: #1 total tags in treatment: 521295 INFO @ Fri, 26 Jun 2020 06:22:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:22:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:22:51: #1 tags after filtering in treatment: 458533 INFO @ Fri, 26 Jun 2020 06:22:51: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 06:22:51: #1 finished! INFO @ Fri, 26 Jun 2020 06:22:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:22:51: #2 number of paired peaks: 1825 INFO @ Fri, 26 Jun 2020 06:22:51: start model_add_line... INFO @ Fri, 26 Jun 2020 06:22:51: start X-correlation... INFO @ Fri, 26 Jun 2020 06:22:51: end of X-cor INFO @ Fri, 26 Jun 2020 06:22:51: #2 finished! INFO @ Fri, 26 Jun 2020 06:22:51: #2 predicted fragment length is 237 bps INFO @ Fri, 26 Jun 2020 06:22:51: #2 alternative fragment length(s) may be 237 bps INFO @ Fri, 26 Jun 2020 06:22:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.10_model.r INFO @ Fri, 26 Jun 2020 06:22:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:22:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:22:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.10_summits.bed INFO @ Fri, 26 Jun 2020 06:22:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (987 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Fri, 26 Jun 2020 06:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Fri, 26 Jun 2020 06:23:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:23:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:23:15: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:23:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:23:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:23:20: #1 total tags in treatment: 521295 INFO @ Fri, 26 Jun 2020 06:23:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:23:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 06:23:20: #1 tags after filtering in treatment: 458533 INFO @ Fri, 26 Jun 2020 06:23:20: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 06:23:20: #1 finished! INFO @ Fri, 26 Jun 2020 06:23:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:23:20: #2 number of paired peaks: 1825 INFO @ Fri, 26 Jun 2020 06:23:20: start model_add_line... INFO @ Fri, 26 Jun 2020 06:23:20: start X-correlation... INFO @ Fri, 26 Jun 2020 06:23:20: end of X-cor INFO @ Fri, 26 Jun 2020 06:23:20: #2 finished! INFO @ Fri, 26 Jun 2020 06:23:20: #2 predicted fragment length is 237 bps INFO @ Fri, 26 Jun 2020 06:23:20: #2 alternative fragment length(s) may be 237 bps INFO @ Fri, 26 Jun 2020 06:23:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.20_model.r INFO @ Fri, 26 Jun 2020 06:23:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:23:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:23:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:23:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:23:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:23:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010106/SRX1010106.20_summits.bed INFO @ Fri, 26 Jun 2020 06:23:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (655 records, 4 fields): 2 millis CompletedMACS2peakCalling