Job ID = 6368368 SRX = SRX495048 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:08:34 prefetch.2.10.7 int: timeout exhausted while creating file within network system module - cannot open remote file: https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1198580/SRR1198580.1 2020-06-16T00:08:39 prefetch.2.10.7: 1) Downloading 'SRR1198580'... 2020-06-16T00:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:09:59 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:09:59 prefetch.2.10.7: 'SRR1198580' is valid 2020-06-16T00:09:59 prefetch.2.10.7: 1) 'SRR1198580' was downloaded successfully Read 14746480 spots for SRR1198580/SRR1198580.sra Written 14746480 spots for SRR1198580/SRR1198580.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: 00:02:22 14746480 reads; of these: 14746480 (100.00%) were unpaired; of these: 2009069 (13.62%) aligned 0 times 10079319 (68.35%) aligned exactly 1 time 2658092 (18.03%) aligned >1 times 86.38% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 3149976 / 12737411 = 0.2473 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 09:15:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.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 09:15:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:02: 1000000 INFO @ Tue, 16 Jun 2020 09:16:07: 2000000 INFO @ Tue, 16 Jun 2020 09:16:12: 3000000 INFO @ Tue, 16 Jun 2020 09:16:18: 4000000 INFO @ Tue, 16 Jun 2020 09:16:23: 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 09:16:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.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 09:16:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:29: 6000000 INFO @ Tue, 16 Jun 2020 09:16:34: 1000000 INFO @ Tue, 16 Jun 2020 09:16:35: 7000000 INFO @ Tue, 16 Jun 2020 09:16:39: 2000000 INFO @ Tue, 16 Jun 2020 09:16:41: 8000000 INFO @ Tue, 16 Jun 2020 09:16:45: 3000000 INFO @ Tue, 16 Jun 2020 09:16:46: 9000000 INFO @ Tue, 16 Jun 2020 09:16:50: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:16:50: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:16:50: #1 total tags in treatment: 9587435 INFO @ Tue, 16 Jun 2020 09:16:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:50: #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 09:16:50: #1 tags after filtering in treatment: 9587435 INFO @ Tue, 16 Jun 2020 09:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:51: #2 number of paired peaks: 612 WARNING @ Tue, 16 Jun 2020 09:16:51: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:51: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 09:16:51: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 09:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.05_model.r INFO @ Tue, 16 Jun 2020 09:16:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:51: 4000000 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 09:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.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 09:16:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:57: 5000000 INFO @ Tue, 16 Jun 2020 09:17:03: 1000000 INFO @ Tue, 16 Jun 2020 09:17:03: 6000000 INFO @ Tue, 16 Jun 2020 09:17:09: 2000000 INFO @ Tue, 16 Jun 2020 09:17:09: 7000000 INFO @ Tue, 16 Jun 2020 09:17:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:15: 3000000 INFO @ Tue, 16 Jun 2020 09:17:15: 8000000 INFO @ Tue, 16 Jun 2020 09:17:21: 4000000 INFO @ Tue, 16 Jun 2020 09:17:21: 9000000 INFO @ Tue, 16 Jun 2020 09:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1492 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:25: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:17:25: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:17:25: #1 total tags in treatment: 9587435 INFO @ Tue, 16 Jun 2020 09:17:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:25: #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 09:17:25: #1 tags after filtering in treatment: 9587435 INFO @ Tue, 16 Jun 2020 09:17:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:26: #2 number of paired peaks: 612 WARNING @ Tue, 16 Jun 2020 09:17:26: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:26: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 09:17:26: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 09:17:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.10_model.r INFO @ Tue, 16 Jun 2020 09:17:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:27: 5000000 INFO @ Tue, 16 Jun 2020 09:17:32: 6000000 INFO @ Tue, 16 Jun 2020 09:17:38: 7000000 INFO @ Tue, 16 Jun 2020 09:17:43: 8000000 INFO @ Tue, 16 Jun 2020 09:17:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:49: 9000000 INFO @ Tue, 16 Jun 2020 09:17:52: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:17:52: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:17:52: #1 total tags in treatment: 9587435 INFO @ Tue, 16 Jun 2020 09:17:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:52: #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 09:17:52: #1 tags after filtering in treatment: 9587435 INFO @ Tue, 16 Jun 2020 09:17:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:53: #2 number of paired peaks: 612 WARNING @ Tue, 16 Jun 2020 09:17:53: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:53: #2 predicted fragment length is 121 bps INFO @ Tue, 16 Jun 2020 09:17:53: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 16 Jun 2020 09:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.20_model.r INFO @ Tue, 16 Jun 2020 09:17:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1099 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495048/SRX495048.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 2 millis CompletedMACS2peakCalling