Job ID = 6366589 SRX = SRX2035136 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:51:11 prefetch.2.10.7: 1) Downloading 'SRR4044260'... 2020-06-15T22:51:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:58 prefetch.2.10.7: 1) 'SRR4044260' was downloaded successfully Read 6460224 spots for SRR4044260/SRR4044260.sra Written 6460224 spots for SRR4044260/SRR4044260.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: 00:08:06 6460224 reads; of these: 6460224 (100.00%) were paired; of these: 1826255 (28.27%) aligned concordantly 0 times 4047337 (62.65%) aligned concordantly exactly 1 time 586632 (9.08%) aligned concordantly >1 times ---- 1826255 pairs aligned concordantly 0 times; of these: 524382 (28.71%) aligned discordantly 1 time ---- 1301873 pairs aligned 0 times concordantly or discordantly; of these: 2603746 mates make up the pairs; of these: 2398037 (92.10%) aligned 0 times 84435 (3.24%) aligned exactly 1 time 121274 (4.66%) aligned >1 times 81.44% overall alignment rate Time searching: 00:08:06 Overall time: 00:08:06 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_sort_core] merging from 8 files... [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] 380021 / 5153932 = 0.0737 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 @ Tue, 16 Jun 2020 08:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.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 @ Tue, 16 Jun 2020 08:07:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:03: 1000000 INFO @ Tue, 16 Jun 2020 08:08:11: 2000000 INFO @ Tue, 16 Jun 2020 08:08:19: 3000000 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 @ Tue, 16 Jun 2020 08:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.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 @ Tue, 16 Jun 2020 08:08:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:26: 4000000 INFO @ Tue, 16 Jun 2020 08:08:34: 1000000 INFO @ Tue, 16 Jun 2020 08:08:35: 5000000 INFO @ Tue, 16 Jun 2020 08:08:43: 2000000 INFO @ Tue, 16 Jun 2020 08:08:44: 6000000 INFO @ Tue, 16 Jun 2020 08:08:52: 3000000 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 @ Tue, 16 Jun 2020 08:08:53: 7000000 INFO @ Tue, 16 Jun 2020 08:08:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.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 @ Tue, 16 Jun 2020 08:08:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:01: 4000000 INFO @ Tue, 16 Jun 2020 08:09:03: 8000000 INFO @ Tue, 16 Jun 2020 08:09:05: 1000000 INFO @ Tue, 16 Jun 2020 08:09:10: 5000000 INFO @ Tue, 16 Jun 2020 08:09:12: 9000000 INFO @ Tue, 16 Jun 2020 08:09:14: 2000000 INFO @ Tue, 16 Jun 2020 08:09:18: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:09:18: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:09:18: #1 total tags in treatment: 4270385 INFO @ Tue, 16 Jun 2020 08:09:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:09:19: #1 tags after filtering in treatment: 3947460 INFO @ Tue, 16 Jun 2020 08:09:19: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:09:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:19: #2 number of paired peaks: 3426 INFO @ Tue, 16 Jun 2020 08:09:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:19: #2 predicted fragment length is 281 bps INFO @ Tue, 16 Jun 2020 08:09:19: #2 alternative fragment length(s) may be 281 bps INFO @ Tue, 16 Jun 2020 08:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.05_model.r INFO @ Tue, 16 Jun 2020 08:09:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:19: 6000000 INFO @ Tue, 16 Jun 2020 08:09:23: 3000000 INFO @ Tue, 16 Jun 2020 08:09:28: 7000000 INFO @ Tue, 16 Jun 2020 08:09:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:32: 4000000 INFO @ Tue, 16 Jun 2020 08:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.05_summits.bed INFO @ Tue, 16 Jun 2020 08:09:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3127 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:37: 8000000 INFO @ Tue, 16 Jun 2020 08:09:41: 5000000 INFO @ Tue, 16 Jun 2020 08:09:46: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:50: 6000000 INFO @ Tue, 16 Jun 2020 08:09:53: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:09:53: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:09:53: #1 total tags in treatment: 4270385 INFO @ Tue, 16 Jun 2020 08:09:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:09:53: #1 tags after filtering in treatment: 3947460 INFO @ Tue, 16 Jun 2020 08:09:53: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:09:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:53: #2 number of paired peaks: 3426 INFO @ Tue, 16 Jun 2020 08:09:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:53: #2 predicted fragment length is 281 bps INFO @ Tue, 16 Jun 2020 08:09:53: #2 alternative fragment length(s) may be 281 bps INFO @ Tue, 16 Jun 2020 08:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.10_model.r INFO @ Tue, 16 Jun 2020 08:09:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:58: 7000000 INFO @ Tue, 16 Jun 2020 08:10:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:07: 8000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.10_summits.bed INFO @ Tue, 16 Jun 2020 08:10:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2569 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:15: 9000000 INFO @ Tue, 16 Jun 2020 08:10:21: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:10:21: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:10:21: #1 total tags in treatment: 4270385 INFO @ Tue, 16 Jun 2020 08:10:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:10:21: #1 tags after filtering in treatment: 3947460 INFO @ Tue, 16 Jun 2020 08:10:21: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:10:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:21: #2 number of paired peaks: 3426 INFO @ Tue, 16 Jun 2020 08:10:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:21: #2 predicted fragment length is 281 bps INFO @ Tue, 16 Jun 2020 08:10:21: #2 alternative fragment length(s) may be 281 bps INFO @ Tue, 16 Jun 2020 08:10:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.20_model.r INFO @ Tue, 16 Jun 2020 08:10:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035136/SRX2035136.20_summits.bed INFO @ Tue, 16 Jun 2020 08:10:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2017 records, 4 fields): 4 millis CompletedMACS2peakCalling