Job ID = 6368095 SRX = SRX466558 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:05:16 prefetch.2.10.7: 1) Downloading 'SRR1163624'... 2020-06-16T00:05:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:06:16 prefetch.2.10.7 int: timeout exhausted while creating file within network system module - Cannot KNSManagerMakeClientRequest: https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR1163624/SRR1163624.1 2020-06-16T00:06:16 prefetch.2.10.7: HTTPS download failed 2020-06-16T00:06:16 prefetch.2.10.7: 1) failed to download SRR1163624 2020-06-16T00:06:27 prefetch.2.10.7: 1) Downloading 'SRR1163624'... 2020-06-16T00:06:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:09:48 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:09:48 prefetch.2.10.7: 1) 'SRR1163624' was downloaded successfully Read 14156918 spots for SRR1163624/SRR1163624.sra Written 14156918 spots for SRR1163624/SRR1163624.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: 00:02:42 14156918 reads; of these: 14156918 (100.00%) were unpaired; of these: 173875 (1.23%) aligned 0 times 12310586 (86.96%) aligned exactly 1 time 1672457 (11.81%) aligned >1 times 98.77% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 3967011 / 13983043 = 0.2837 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 09:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.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 09:16:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:43: 1000000 INFO @ Tue, 16 Jun 2020 09:16:48: 2000000 INFO @ Tue, 16 Jun 2020 09:16:54: 3000000 INFO @ Tue, 16 Jun 2020 09:16:59: 4000000 INFO @ Tue, 16 Jun 2020 09:17:04: 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 09:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.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 09:17:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:10: 6000000 INFO @ Tue, 16 Jun 2020 09:17:14: 1000000 INFO @ Tue, 16 Jun 2020 09:17:16: 7000000 INFO @ Tue, 16 Jun 2020 09:17:19: 2000000 INFO @ Tue, 16 Jun 2020 09:17:21: 8000000 INFO @ Tue, 16 Jun 2020 09:17:25: 3000000 INFO @ Tue, 16 Jun 2020 09:17:27: 9000000 INFO @ Tue, 16 Jun 2020 09:17:31: 4000000 INFO @ Tue, 16 Jun 2020 09:17:33: 10000000 INFO @ Tue, 16 Jun 2020 09:17:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:17:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:17:33: #1 total tags in treatment: 10016032 INFO @ Tue, 16 Jun 2020 09:17:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:33: #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 09:17:33: #1 tags after filtering in treatment: 10016032 INFO @ Tue, 16 Jun 2020 09:17:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:34: #2 number of paired peaks: 2348 INFO @ Tue, 16 Jun 2020 09:17:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:34: #2 predicted fragment length is 262 bps INFO @ Tue, 16 Jun 2020 09:17:34: #2 alternative fragment length(s) may be 4,262 bps INFO @ Tue, 16 Jun 2020 09:17:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.05_model.r INFO @ Tue, 16 Jun 2020 09:17:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:34: #3 Pre-compute pvalue-qvalue table... 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 09:17:37: 5000000 INFO @ Tue, 16 Jun 2020 09:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.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 09:17:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:43: 6000000 INFO @ Tue, 16 Jun 2020 09:17:44: 1000000 INFO @ Tue, 16 Jun 2020 09:17:49: 7000000 INFO @ Tue, 16 Jun 2020 09:17:51: 2000000 INFO @ Tue, 16 Jun 2020 09:17:55: 8000000 INFO @ Tue, 16 Jun 2020 09:17:57: 3000000 INFO @ Tue, 16 Jun 2020 09:18:01: 9000000 INFO @ Tue, 16 Jun 2020 09:18:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:03: 4000000 INFO @ Tue, 16 Jun 2020 09:18:08: 10000000 INFO @ Tue, 16 Jun 2020 09:18:08: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:18:08: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:18:08: #1 total tags in treatment: 10016032 INFO @ Tue, 16 Jun 2020 09:18:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:08: #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 09:18:08: #1 tags after filtering in treatment: 10016032 INFO @ Tue, 16 Jun 2020 09:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:09: #2 number of paired peaks: 2348 INFO @ Tue, 16 Jun 2020 09:18:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:09: #2 predicted fragment length is 262 bps INFO @ Tue, 16 Jun 2020 09:18:09: #2 alternative fragment length(s) may be 4,262 bps INFO @ Tue, 16 Jun 2020 09:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.10_model.r INFO @ Tue, 16 Jun 2020 09:18:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:09: 5000000 INFO @ Tue, 16 Jun 2020 09:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.05_summits.bed INFO @ Tue, 16 Jun 2020 09:18:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4240 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:18:15: 6000000 INFO @ Tue, 16 Jun 2020 09:18:21: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:18:26: 8000000 INFO @ Tue, 16 Jun 2020 09:18:32: 9000000 INFO @ Tue, 16 Jun 2020 09:18:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:38: 10000000 INFO @ Tue, 16 Jun 2020 09:18:38: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:18:38: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:18:38: #1 total tags in treatment: 10016032 INFO @ Tue, 16 Jun 2020 09:18:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:38: #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 09:18:38: #1 tags after filtering in treatment: 10016032 INFO @ Tue, 16 Jun 2020 09:18:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:18:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:39: #2 number of paired peaks: 2348 INFO @ Tue, 16 Jun 2020 09:18:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:39: #2 predicted fragment length is 262 bps INFO @ Tue, 16 Jun 2020 09:18:39: #2 alternative fragment length(s) may be 4,262 bps INFO @ Tue, 16 Jun 2020 09:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.20_model.r INFO @ Tue, 16 Jun 2020 09:18:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.10_summits.bed INFO @ Tue, 16 Jun 2020 09:18:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2543 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466558/SRX466558.20_summits.bed INFO @ Tue, 16 Jun 2020 09:19:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1236 records, 4 fields): 4 millis CompletedMACS2peakCalling