Job ID = 6366918 SRX = SRX2576621 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:23 prefetch.2.10.7: 1) Downloading 'SRR5272578'... 2020-06-15T23:01:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:33 prefetch.2.10.7: 'SRR5272578' is valid 2020-06-15T23:02:33 prefetch.2.10.7: 1) 'SRR5272578' was downloaded successfully Read 16135860 spots for SRR5272578/SRR5272578.sra Written 16135860 spots for SRR5272578/SRR5272578.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: 00:02:32 16135860 reads; of these: 16135860 (100.00%) were unpaired; of these: 2430564 (15.06%) aligned 0 times 11466637 (71.06%) aligned exactly 1 time 2238659 (13.87%) aligned >1 times 84.94% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 3440951 / 13705296 = 0.2511 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 08:08:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.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 08:08:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:05: 1000000 INFO @ Tue, 16 Jun 2020 08:09:11: 2000000 INFO @ Tue, 16 Jun 2020 08:09:16: 3000000 INFO @ Tue, 16 Jun 2020 08:09:22: 4000000 INFO @ Tue, 16 Jun 2020 08:09:27: 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 08:09:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.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 08:09:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:33: 6000000 INFO @ Tue, 16 Jun 2020 08:09:35: 1000000 INFO @ Tue, 16 Jun 2020 08:09:39: 7000000 INFO @ Tue, 16 Jun 2020 08:09:41: 2000000 INFO @ Tue, 16 Jun 2020 08:09:44: 8000000 INFO @ Tue, 16 Jun 2020 08:09:46: 3000000 INFO @ Tue, 16 Jun 2020 08:09:50: 9000000 INFO @ Tue, 16 Jun 2020 08:09:52: 4000000 INFO @ Tue, 16 Jun 2020 08:09:56: 10000000 INFO @ Tue, 16 Jun 2020 08:09:57: 5000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:09:58: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:09:58: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:09:58: #1 total tags in treatment: 10264345 INFO @ Tue, 16 Jun 2020 08:09:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 08:09:58: #1 tags after filtering in treatment: 10264345 INFO @ Tue, 16 Jun 2020 08:09:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:58: #2 number of paired peaks: 913 WARNING @ Tue, 16 Jun 2020 08:09:58: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:59: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 08:09:59: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 08:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.05_model.r INFO @ Tue, 16 Jun 2020 08:09:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.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 08:09:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:03: 6000000 INFO @ Tue, 16 Jun 2020 08:10:05: 1000000 INFO @ Tue, 16 Jun 2020 08:10:09: 7000000 INFO @ Tue, 16 Jun 2020 08:10:11: 2000000 INFO @ Tue, 16 Jun 2020 08:10:14: 8000000 INFO @ Tue, 16 Jun 2020 08:10:16: 3000000 INFO @ Tue, 16 Jun 2020 08:10:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:20: 9000000 INFO @ Tue, 16 Jun 2020 08:10:22: 4000000 INFO @ Tue, 16 Jun 2020 08:10:26: 10000000 INFO @ Tue, 16 Jun 2020 08:10:27: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:10:27: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:10:27: #1 total tags in treatment: 10264345 INFO @ Tue, 16 Jun 2020 08:10:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:27: #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 08:10:28: #1 tags after filtering in treatment: 10264345 INFO @ Tue, 16 Jun 2020 08:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:28: 5000000 INFO @ Tue, 16 Jun 2020 08:10:28: #2 number of paired peaks: 913 WARNING @ Tue, 16 Jun 2020 08:10:28: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:28: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 08:10:28: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 08:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.10_model.r INFO @ Tue, 16 Jun 2020 08:10:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.05_summits.bed INFO @ Tue, 16 Jun 2020 08:10:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5537 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:33: 6000000 INFO @ Tue, 16 Jun 2020 08:10:39: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:10:44: 8000000 INFO @ Tue, 16 Jun 2020 08:10:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:50: 9000000 INFO @ Tue, 16 Jun 2020 08:10:55: 10000000 INFO @ Tue, 16 Jun 2020 08:10:57: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:10:57: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:10:57: #1 total tags in treatment: 10264345 INFO @ Tue, 16 Jun 2020 08:10:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:57: #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 08:10:57: #1 tags after filtering in treatment: 10264345 INFO @ Tue, 16 Jun 2020 08:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:58: #2 number of paired peaks: 913 WARNING @ Tue, 16 Jun 2020 08:10:58: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:58: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 08:10:58: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 08:10:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.20_model.r INFO @ Tue, 16 Jun 2020 08:10:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.10_summits.bed INFO @ Tue, 16 Jun 2020 08:10:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3522 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576621/SRX2576621.20_summits.bed INFO @ Tue, 16 Jun 2020 08:11:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2292 records, 4 fields): 4 millis CompletedMACS2peakCalling