Job ID = 6366670 SRX = SRX2202783 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:38 prefetch.2.10.7: 1) Downloading 'SRR4319289'... 2020-06-15T22:57:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:18 prefetch.2.10.7: 'SRR4319289' is valid 2020-06-15T22:58:18 prefetch.2.10.7: 1) 'SRR4319289' was downloaded successfully 2020-06-15T22:58:51 prefetch.2.10.7: 'SRR4319289' has 6 unresolved dependencies 2020-06-15T22:58:51 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T22:58:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:07 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:59:07 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T22:59:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:23 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:59:23 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T22:59:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:38 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:59:38 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T22:59:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:54 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T22:59:54 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T22:59:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:12 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:00:12 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T23:00:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:27 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 20182598 spots for SRR4319289/SRR4319289.sra Written 20182598 spots for SRR4319289/SRR4319289.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: 00:04:03 20182598 reads; of these: 20182598 (100.00%) were unpaired; of these: 1496897 (7.42%) aligned 0 times 11668596 (57.82%) aligned exactly 1 time 7017105 (34.77%) aligned >1 times 92.58% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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_rmdupse_core] 6760268 / 18685701 = 0.3618 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 08:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.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 08:09:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:41: 1000000 INFO @ Tue, 16 Jun 2020 08:09:47: 2000000 INFO @ Tue, 16 Jun 2020 08:09:53: 3000000 INFO @ Tue, 16 Jun 2020 08:09:59: 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 @ Tue, 16 Jun 2020 08:10:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.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 08:10:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:05: 5000000 INFO @ Tue, 16 Jun 2020 08:10:12: 6000000 INFO @ Tue, 16 Jun 2020 08:10:13: 1000000 INFO @ Tue, 16 Jun 2020 08:10:20: 7000000 INFO @ Tue, 16 Jun 2020 08:10:21: 2000000 INFO @ Tue, 16 Jun 2020 08:10:28: 8000000 INFO @ Tue, 16 Jun 2020 08:10:30: 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 08:10:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.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 08:10:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:36: 9000000 INFO @ Tue, 16 Jun 2020 08:10:38: 4000000 INFO @ Tue, 16 Jun 2020 08:10:43: 1000000 INFO @ Tue, 16 Jun 2020 08:10:44: 10000000 INFO @ Tue, 16 Jun 2020 08:10:46: 5000000 INFO @ Tue, 16 Jun 2020 08:10:50: 2000000 INFO @ Tue, 16 Jun 2020 08:10:51: 11000000 INFO @ Tue, 16 Jun 2020 08:10:55: 6000000 INFO @ Tue, 16 Jun 2020 08:10:58: 3000000 INFO @ Tue, 16 Jun 2020 08:10:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:10:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:10:58: #1 total tags in treatment: 11925433 INFO @ Tue, 16 Jun 2020 08:10:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:58: #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 08:10:59: #1 tags after filtering in treatment: 11925433 INFO @ Tue, 16 Jun 2020 08:10:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:00: #2 number of paired peaks: 3976 INFO @ Tue, 16 Jun 2020 08:11:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:00: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 08:11:00: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 08:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.05_model.r INFO @ Tue, 16 Jun 2020 08:11:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:03: 7000000 INFO @ Tue, 16 Jun 2020 08:11:06: 4000000 INFO @ Tue, 16 Jun 2020 08:11:12: 8000000 INFO @ Tue, 16 Jun 2020 08:11:13: 5000000 INFO @ Tue, 16 Jun 2020 08:11:20: 9000000 INFO @ Tue, 16 Jun 2020 08:11:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:29: 10000000 INFO @ Tue, 16 Jun 2020 08:11:29: 7000000 INFO @ Tue, 16 Jun 2020 08:11:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:37: 8000000 INFO @ Tue, 16 Jun 2020 08:11:37: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:45: 9000000 INFO @ Tue, 16 Jun 2020 08:11:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:45: #1 total tags in treatment: 11925433 INFO @ Tue, 16 Jun 2020 08:11:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:45: #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 08:11:45: #1 tags after filtering in treatment: 11925433 INFO @ Tue, 16 Jun 2020 08:11:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:47: #2 number of paired peaks: 3976 INFO @ Tue, 16 Jun 2020 08:11:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:47: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 08:11:47: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 08:11:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.10_model.r INFO @ Tue, 16 Jun 2020 08:11:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (12092 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:51: 10000000 INFO @ Tue, 16 Jun 2020 08:11:57: 11000000 INFO @ Tue, 16 Jun 2020 08:12:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:03: #1 total tags in treatment: 11925433 INFO @ Tue, 16 Jun 2020 08:12:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:03: #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 08:12:03: #1 tags after filtering in treatment: 11925433 INFO @ Tue, 16 Jun 2020 08:12:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:04: #2 number of paired peaks: 3976 INFO @ Tue, 16 Jun 2020 08:12:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:04: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 08:12:04: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 08:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.20_model.r INFO @ Tue, 16 Jun 2020 08:12:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.10_summits.bed INFO @ Tue, 16 Jun 2020 08:12:35: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (8815 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202783/SRX2202783.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5244 records, 4 fields): 6 millis CompletedMACS2peakCalling