Job ID = 14160621 SRX = SRX10399035 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15240550 spots for SRR14022423/SRR14022423.sra Written 15240550 spots for SRR14022423/SRR14022423.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160753 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:34 15240550 reads; of these: 15240550 (100.00%) were unpaired; of these: 2823554 (18.53%) aligned 0 times 10205579 (66.96%) aligned exactly 1 time 2211417 (14.51%) aligned >1 times 81.47% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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] 2152490 / 12416996 = 0.1734 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:34:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.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 @ Thu, 09 Dec 2021 03:34:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:34:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:34:40: 1000000 INFO @ Thu, 09 Dec 2021 03:34:47: 2000000 INFO @ Thu, 09 Dec 2021 03:34:53: 3000000 INFO @ Thu, 09 Dec 2021 03:34:59: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.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 @ Thu, 09 Dec 2021 03:35:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:35:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:35:07: 5000000 INFO @ Thu, 09 Dec 2021 03:35:12: 1000000 INFO @ Thu, 09 Dec 2021 03:35:14: 6000000 INFO @ Thu, 09 Dec 2021 03:35:20: 2000000 INFO @ Thu, 09 Dec 2021 03:35:22: 7000000 INFO @ Thu, 09 Dec 2021 03:35:29: 3000000 INFO @ Thu, 09 Dec 2021 03:35:29: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:35:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.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 @ Thu, 09 Dec 2021 03:35:32: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:35:32: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:35:36: 9000000 INFO @ Thu, 09 Dec 2021 03:35:37: 4000000 INFO @ Thu, 09 Dec 2021 03:35:41: 1000000 INFO @ Thu, 09 Dec 2021 03:35:44: 10000000 INFO @ Thu, 09 Dec 2021 03:35:46: 5000000 INFO @ Thu, 09 Dec 2021 03:35:46: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:35:46: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:35:46: #1 total tags in treatment: 10264506 INFO @ Thu, 09 Dec 2021 03:35:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:35:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:35:46: #1 tags after filtering in treatment: 10264506 INFO @ Thu, 09 Dec 2021 03:35:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:35:46: #1 finished! INFO @ Thu, 09 Dec 2021 03:35:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:35:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:35:47: #2 number of paired peaks: 595 WARNING @ Thu, 09 Dec 2021 03:35:47: Fewer paired peaks (595) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 595 pairs to build model! INFO @ Thu, 09 Dec 2021 03:35:47: start model_add_line... INFO @ Thu, 09 Dec 2021 03:35:47: start X-correlation... INFO @ Thu, 09 Dec 2021 03:35:47: end of X-cor INFO @ Thu, 09 Dec 2021 03:35:47: #2 finished! INFO @ Thu, 09 Dec 2021 03:35:47: #2 predicted fragment length is 190 bps INFO @ Thu, 09 Dec 2021 03:35:47: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 09 Dec 2021 03:35:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.05_model.r INFO @ Thu, 09 Dec 2021 03:35:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:35:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:35:49: 2000000 INFO @ Thu, 09 Dec 2021 03:35:54: 6000000 INFO @ Thu, 09 Dec 2021 03:35:58: 3000000 INFO @ Thu, 09 Dec 2021 03:36:02: 7000000 INFO @ Thu, 09 Dec 2021 03:36:06: 4000000 INFO @ Thu, 09 Dec 2021 03:36:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:36:11: 8000000 INFO @ Thu, 09 Dec 2021 03:36:14: 5000000 INFO @ Thu, 09 Dec 2021 03:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.05_summits.bed INFO @ Thu, 09 Dec 2021 03:36:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2072 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:36:19: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:36:22: 6000000 INFO @ Thu, 09 Dec 2021 03:36:27: 10000000 INFO @ Thu, 09 Dec 2021 03:36:29: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:36:29: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:36:29: #1 total tags in treatment: 10264506 INFO @ Thu, 09 Dec 2021 03:36:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:36:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:36:29: #1 tags after filtering in treatment: 10264506 INFO @ Thu, 09 Dec 2021 03:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:36:29: #1 finished! INFO @ Thu, 09 Dec 2021 03:36:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:36:30: #2 number of paired peaks: 595 WARNING @ Thu, 09 Dec 2021 03:36:30: Fewer paired peaks (595) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 595 pairs to build model! INFO @ Thu, 09 Dec 2021 03:36:30: start model_add_line... INFO @ Thu, 09 Dec 2021 03:36:30: start X-correlation... INFO @ Thu, 09 Dec 2021 03:36:30: end of X-cor INFO @ Thu, 09 Dec 2021 03:36:30: #2 finished! INFO @ Thu, 09 Dec 2021 03:36:30: #2 predicted fragment length is 190 bps INFO @ Thu, 09 Dec 2021 03:36:30: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 09 Dec 2021 03:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.10_model.r INFO @ Thu, 09 Dec 2021 03:36:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:36:31: 7000000 INFO @ Thu, 09 Dec 2021 03:36:39: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:36:46: 9000000 INFO @ Thu, 09 Dec 2021 03:36:51: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:36:54: 10000000 INFO @ Thu, 09 Dec 2021 03:36:55: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:36:55: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:36:55: #1 total tags in treatment: 10264506 INFO @ Thu, 09 Dec 2021 03:36:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:36:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:36:56: #1 tags after filtering in treatment: 10264506 INFO @ Thu, 09 Dec 2021 03:36:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:36:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:36:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:36:56: #2 number of paired peaks: 595 WARNING @ Thu, 09 Dec 2021 03:36:56: Fewer paired peaks (595) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 595 pairs to build model! INFO @ Thu, 09 Dec 2021 03:36:56: start model_add_line... INFO @ Thu, 09 Dec 2021 03:36:56: start X-correlation... INFO @ Thu, 09 Dec 2021 03:36:56: end of X-cor INFO @ Thu, 09 Dec 2021 03:36:56: #2 finished! INFO @ Thu, 09 Dec 2021 03:36:56: #2 predicted fragment length is 190 bps INFO @ Thu, 09 Dec 2021 03:36:56: #2 alternative fragment length(s) may be 190 bps INFO @ Thu, 09 Dec 2021 03:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.20_model.r INFO @ Thu, 09 Dec 2021 03:36:56: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:37:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.10_summits.bed INFO @ Thu, 09 Dec 2021 03:37:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1322 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:37:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:37:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:37:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:37:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399035/SRX10399035.20_summits.bed INFO @ Thu, 09 Dec 2021 03:37:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (782 records, 4 fields): 2 millis CompletedMACS2peakCalling