Job ID = 6365887 SRX = SRX005651 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:28:44 prefetch.2.10.7: 1) Downloading 'SRR017620'... 2020-06-15T22:28:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:29:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:29:19 prefetch.2.10.7: 'SRR017620' is valid 2020-06-15T22:29:19 prefetch.2.10.7: 1) 'SRR017620' was downloaded successfully Read 6387040 spots for SRR017620/SRR017620.sra Written 6387040 spots for SRR017620/SRR017620.sra 2020-06-15T22:29:46 prefetch.2.10.7: 1) Downloading 'SRR017621'... 2020-06-15T22:29:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:20 prefetch.2.10.7: 'SRR017621' is valid 2020-06-15T22:30:20 prefetch.2.10.7: 1) 'SRR017621' was downloaded successfully Read 6285680 spots for SRR017621/SRR017621.sra Written 6285680 spots for SRR017621/SRR017621.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: 00:01:47 12672720 reads; of these: 12672720 (100.00%) were unpaired; of these: 1757642 (13.87%) aligned 0 times 9463525 (74.68%) aligned exactly 1 time 1451553 (11.45%) aligned >1 times 86.13% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 1248587 / 10915078 = 0.1144 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 07:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.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 07:35:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:15: 1000000 INFO @ Tue, 16 Jun 2020 07:35:20: 2000000 INFO @ Tue, 16 Jun 2020 07:35:25: 3000000 INFO @ Tue, 16 Jun 2020 07:35:30: 4000000 INFO @ Tue, 16 Jun 2020 07:35:35: 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 @ Tue, 16 Jun 2020 07:35:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.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 07:35:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:40: 6000000 INFO @ Tue, 16 Jun 2020 07:35:44: 1000000 INFO @ Tue, 16 Jun 2020 07:35:45: 7000000 INFO @ Tue, 16 Jun 2020 07:35:50: 2000000 INFO @ Tue, 16 Jun 2020 07:35:51: 8000000 INFO @ Tue, 16 Jun 2020 07:35:55: 3000000 INFO @ Tue, 16 Jun 2020 07:35:56: 9000000 INFO @ Tue, 16 Jun 2020 07:36:00: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:36:00: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:36:00: #1 total tags in treatment: 9666491 INFO @ Tue, 16 Jun 2020 07:36:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:00: #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 07:36:00: #1 tags after filtering in treatment: 9666491 INFO @ Tue, 16 Jun 2020 07:36:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:01: #2 number of paired peaks: 1228 INFO @ Tue, 16 Jun 2020 07:36:01: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:01: 4000000 INFO @ Tue, 16 Jun 2020 07:36:01: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:01: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:01: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:01: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:36:01: #2 alternative fragment length(s) may be 4,101 bps INFO @ Tue, 16 Jun 2020 07:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.05_model.r INFO @ Tue, 16 Jun 2020 07:36:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:06: 5000000 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 07:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.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 07:36:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:11: 6000000 INFO @ Tue, 16 Jun 2020 07:36:14: 1000000 INFO @ Tue, 16 Jun 2020 07:36:16: 7000000 INFO @ Tue, 16 Jun 2020 07:36:20: 2000000 INFO @ Tue, 16 Jun 2020 07:36:22: 8000000 INFO @ Tue, 16 Jun 2020 07:36:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:25: 3000000 INFO @ Tue, 16 Jun 2020 07:36:27: 9000000 INFO @ Tue, 16 Jun 2020 07:36:30: 4000000 INFO @ Tue, 16 Jun 2020 07:36:31: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:36:31: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:36:31: #1 total tags in treatment: 9666491 INFO @ Tue, 16 Jun 2020 07:36:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:31: #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 07:36:31: #1 tags after filtering in treatment: 9666491 INFO @ Tue, 16 Jun 2020 07:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:31: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:32: #2 number of paired peaks: 1228 INFO @ Tue, 16 Jun 2020 07:36:32: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:32: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:32: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:32: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:32: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:36:32: #2 alternative fragment length(s) may be 4,101 bps INFO @ Tue, 16 Jun 2020 07:36:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.10_model.r INFO @ Tue, 16 Jun 2020 07:36:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:35: 5000000 INFO @ Tue, 16 Jun 2020 07:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.05_summits.bed INFO @ Tue, 16 Jun 2020 07:36:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4966 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:36:40: 6000000 INFO @ Tue, 16 Jun 2020 07:36:45: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:36:51: 8000000 INFO @ Tue, 16 Jun 2020 07:36:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:56: 9000000 INFO @ Tue, 16 Jun 2020 07:36:59: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:36:59: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:36:59: #1 total tags in treatment: 9666491 INFO @ Tue, 16 Jun 2020 07:36:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:59: #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 07:36:59: #1 tags after filtering in treatment: 9666491 INFO @ Tue, 16 Jun 2020 07:36:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:59: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:00: #2 number of paired peaks: 1228 INFO @ Tue, 16 Jun 2020 07:37:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:00: #2 predicted fragment length is 101 bps INFO @ Tue, 16 Jun 2020 07:37:00: #2 alternative fragment length(s) may be 4,101 bps INFO @ Tue, 16 Jun 2020 07:37:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.20_model.r INFO @ Tue, 16 Jun 2020 07:37:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.10_summits.bed INFO @ Tue, 16 Jun 2020 07:37:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2416 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:37:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005651/SRX005651.20_summits.bed INFO @ Tue, 16 Jun 2020 07:37:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 2 millis CompletedMACS2peakCalling