Job ID = 14160574 SRX = SRX10399016 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16652358 spots for SRR14022404/SRR14022404.sra Written 16652358 spots for SRR14022404/SRR14022404.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160699 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:49 16652358 reads; of these: 16652358 (100.00%) were unpaired; of these: 3931922 (23.61%) aligned 0 times 10756931 (64.60%) aligned exactly 1 time 1963505 (11.79%) aligned >1 times 76.39% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 2928780 / 12720436 = 0.2302 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 03:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.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 03:25:57: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:25:57: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:26:06: 1000000 INFO @ Thu, 09 Dec 2021 03:26:15: 2000000 INFO @ Thu, 09 Dec 2021 03:26:23: 3000000 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 03:26:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.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 03:26:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:26:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:26:31: 4000000 INFO @ Thu, 09 Dec 2021 03:26:36: 1000000 INFO @ Thu, 09 Dec 2021 03:26:40: 5000000 INFO @ Thu, 09 Dec 2021 03:26:47: 2000000 INFO @ Thu, 09 Dec 2021 03:26:48: 6000000 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 03:26:55: 3000000 INFO @ Thu, 09 Dec 2021 03:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.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 03:26:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:26:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:26:57: 7000000 INFO @ Thu, 09 Dec 2021 03:27:04: 4000000 INFO @ Thu, 09 Dec 2021 03:27:05: 8000000 INFO @ Thu, 09 Dec 2021 03:27:06: 1000000 INFO @ Thu, 09 Dec 2021 03:27:12: 5000000 INFO @ Thu, 09 Dec 2021 03:27:14: 9000000 INFO @ Thu, 09 Dec 2021 03:27:17: 2000000 INFO @ Thu, 09 Dec 2021 03:27:21: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:27:21: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:27:21: #1 total tags in treatment: 9791656 INFO @ Thu, 09 Dec 2021 03:27:21: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:27:21: #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 03:27:21: #1 tags after filtering in treatment: 9791656 INFO @ Thu, 09 Dec 2021 03:27:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:27:21: #1 finished! INFO @ Thu, 09 Dec 2021 03:27:21: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:27:21: 6000000 INFO @ Thu, 09 Dec 2021 03:27:21: #2 number of paired peaks: 698 WARNING @ Thu, 09 Dec 2021 03:27:21: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Thu, 09 Dec 2021 03:27:21: start model_add_line... INFO @ Thu, 09 Dec 2021 03:27:22: start X-correlation... INFO @ Thu, 09 Dec 2021 03:27:22: end of X-cor INFO @ Thu, 09 Dec 2021 03:27:22: #2 finished! INFO @ Thu, 09 Dec 2021 03:27:22: #2 predicted fragment length is 156 bps INFO @ Thu, 09 Dec 2021 03:27:22: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 09 Dec 2021 03:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.05_model.r INFO @ Thu, 09 Dec 2021 03:27:22: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:27:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:27:26: 3000000 INFO @ Thu, 09 Dec 2021 03:27:29: 7000000 INFO @ Thu, 09 Dec 2021 03:27:36: 4000000 INFO @ Thu, 09 Dec 2021 03:27:37: 8000000 INFO @ Thu, 09 Dec 2021 03:27:45: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:27:46: 9000000 INFO @ Thu, 09 Dec 2021 03:27:46: 5000000 INFO @ Thu, 09 Dec 2021 03:27:52: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:27:52: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:27:52: #1 total tags in treatment: 9791656 INFO @ Thu, 09 Dec 2021 03:27:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:27:52: #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 03:27:52: #1 tags after filtering in treatment: 9791656 INFO @ Thu, 09 Dec 2021 03:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:27:52: #1 finished! INFO @ Thu, 09 Dec 2021 03:27:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:27:53: #2 number of paired peaks: 698 WARNING @ Thu, 09 Dec 2021 03:27:53: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Thu, 09 Dec 2021 03:27:53: start model_add_line... INFO @ Thu, 09 Dec 2021 03:27:53: start X-correlation... INFO @ Thu, 09 Dec 2021 03:27:53: end of X-cor INFO @ Thu, 09 Dec 2021 03:27:53: #2 finished! INFO @ Thu, 09 Dec 2021 03:27:53: #2 predicted fragment length is 156 bps INFO @ Thu, 09 Dec 2021 03:27:53: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 09 Dec 2021 03:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.10_model.r INFO @ Thu, 09 Dec 2021 03:27:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:27:56: 6000000 INFO @ Thu, 09 Dec 2021 03:27:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:27:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:27:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.05_summits.bed INFO @ Thu, 09 Dec 2021 03:27:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2047 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:28:06: 7000000 INFO @ Thu, 09 Dec 2021 03:28:16: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:28:16: 8000000 INFO @ Thu, 09 Dec 2021 03:28:26: 9000000 INFO @ Thu, 09 Dec 2021 03:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:28:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:28:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.10_summits.bed INFO @ Thu, 09 Dec 2021 03:28:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1309 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:28:34: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:28:34: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:28:34: #1 total tags in treatment: 9791656 INFO @ Thu, 09 Dec 2021 03:28:34: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:28:34: #1 tags after filtering in treatment: 9791656 INFO @ Thu, 09 Dec 2021 03:28:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:28:34: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:34: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:35: #2 number of paired peaks: 698 WARNING @ Thu, 09 Dec 2021 03:28:35: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Thu, 09 Dec 2021 03:28:35: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:35: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:35: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:35: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:35: #2 predicted fragment length is 156 bps INFO @ Thu, 09 Dec 2021 03:28:35: #2 alternative fragment length(s) may be 156 bps INFO @ Thu, 09 Dec 2021 03:28:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.20_model.r INFO @ Thu, 09 Dec 2021 03:28:35: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:28:59: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399016/SRX10399016.20_summits.bed INFO @ Thu, 09 Dec 2021 03:29:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (843 records, 4 fields): 4 millis CompletedMACS2peakCalling