Job ID = 6366595 SRX = SRX208764 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:59 prefetch.2.10.7: 1) Downloading 'SRR628898'... 2020-06-15T22:56:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:46 prefetch.2.10.7: 'SRR628898' is valid 2020-06-15T22:57:46 prefetch.2.10.7: 1) 'SRR628898' was downloaded successfully Read 14746480 spots for SRR628898/SRR628898.sra Written 14746480 spots for SRR628898/SRR628898.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: 00:02:18 14746480 reads; of these: 14746480 (100.00%) were unpaired; of these: 2021451 (13.71%) aligned 0 times 10133582 (68.72%) aligned exactly 1 time 2591447 (17.57%) aligned >1 times 86.29% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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_rmdupse_core] 3138744 / 12725029 = 0.2467 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 08:03:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.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 08:03:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:42: 1000000 INFO @ Tue, 16 Jun 2020 08:03:47: 2000000 INFO @ Tue, 16 Jun 2020 08:03:51: 3000000 INFO @ Tue, 16 Jun 2020 08:03:55: 4000000 INFO @ Tue, 16 Jun 2020 08:04:00: 5000000 INFO @ Tue, 16 Jun 2020 08:04:04: 6000000 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 08:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.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 08:04:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:08: 7000000 INFO @ Tue, 16 Jun 2020 08:04:12: 1000000 INFO @ Tue, 16 Jun 2020 08:04:13: 8000000 INFO @ Tue, 16 Jun 2020 08:04:17: 2000000 INFO @ Tue, 16 Jun 2020 08:04:17: 9000000 INFO @ Tue, 16 Jun 2020 08:04:20: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:04:20: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:04:20: #1 total tags in treatment: 9586285 INFO @ Tue, 16 Jun 2020 08:04:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:20: #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 08:04:20: #1 tags after filtering in treatment: 9586285 INFO @ Tue, 16 Jun 2020 08:04:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:21: #2 number of paired peaks: 600 WARNING @ Tue, 16 Jun 2020 08:04:21: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:21: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:04:21: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.05_model.r INFO @ Tue, 16 Jun 2020 08:04:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:21: 3000000 INFO @ Tue, 16 Jun 2020 08:04:26: 4000000 INFO @ Tue, 16 Jun 2020 08:04:30: 5000000 INFO @ Tue, 16 Jun 2020 08:04:35: 6000000 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 08:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.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 08:04:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:39: 7000000 INFO @ Tue, 16 Jun 2020 08:04:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:44: 1000000 INFO @ Tue, 16 Jun 2020 08:04:44: 8000000 INFO @ Tue, 16 Jun 2020 08:04:48: 9000000 INFO @ Tue, 16 Jun 2020 08:04:49: 2000000 INFO @ Tue, 16 Jun 2020 08:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1479 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:51: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:04:51: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:04:51: #1 total tags in treatment: 9586285 INFO @ Tue, 16 Jun 2020 08:04:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:51: #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 08:04:51: #1 tags after filtering in treatment: 9586285 INFO @ Tue, 16 Jun 2020 08:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:52: #2 number of paired peaks: 600 WARNING @ Tue, 16 Jun 2020 08:04:52: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:52: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:04:52: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.10_model.r INFO @ Tue, 16 Jun 2020 08:04:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:54: 3000000 INFO @ Tue, 16 Jun 2020 08:05:00: 4000000 INFO @ Tue, 16 Jun 2020 08:05:05: 5000000 INFO @ Tue, 16 Jun 2020 08:05:10: 6000000 INFO @ Tue, 16 Jun 2020 08:05:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:15: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:05:20: 8000000 INFO @ Tue, 16 Jun 2020 08:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.10_summits.bed INFO @ Tue, 16 Jun 2020 08:05:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1116 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:25: 9000000 INFO @ Tue, 16 Jun 2020 08:05:29: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:05:29: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:05:29: #1 total tags in treatment: 9586285 INFO @ Tue, 16 Jun 2020 08:05:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:29: #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 08:05:29: #1 tags after filtering in treatment: 9586285 INFO @ Tue, 16 Jun 2020 08:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:29: #2 number of paired peaks: 600 WARNING @ Tue, 16 Jun 2020 08:05:29: Fewer paired peaks (600) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 600 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:29: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:05:29: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:05:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.20_model.r INFO @ Tue, 16 Jun 2020 08:05:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208764/SRX208764.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (765 records, 4 fields): 3 millis CompletedMACS2peakCalling