Job ID = 10165834 SRX = SRX8832069 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:58 14729232 reads; of these: 14729232 (100.00%) were unpaired; of these: 688927 (4.68%) aligned 0 times 11959862 (81.20%) aligned exactly 1 time 2080443 (14.12%) aligned >1 times 95.32% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 1740818 / 14040305 = 0.1240 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 @ Thu, 08 Oct 2020 20:05:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.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, 08 Oct 2020 20:05:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:20: 1000000 INFO @ Thu, 08 Oct 2020 20:05:25: 2000000 INFO @ Thu, 08 Oct 2020 20:05:30: 3000000 INFO @ Thu, 08 Oct 2020 20:05:35: 4000000 INFO @ Thu, 08 Oct 2020 20:05:40: 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 @ Thu, 08 Oct 2020 20:05:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.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, 08 Oct 2020 20:05:44: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:44: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:46: 6000000 INFO @ Thu, 08 Oct 2020 20:05:50: 1000000 INFO @ Thu, 08 Oct 2020 20:05:51: 7000000 INFO @ Thu, 08 Oct 2020 20:05:55: 2000000 INFO @ Thu, 08 Oct 2020 20:05:57: 8000000 INFO @ Thu, 08 Oct 2020 20:06:01: 3000000 INFO @ Thu, 08 Oct 2020 20:06:02: 9000000 INFO @ Thu, 08 Oct 2020 20:06:07: 4000000 INFO @ Thu, 08 Oct 2020 20:06:08: 10000000 INFO @ Thu, 08 Oct 2020 20:06:12: 5000000 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 @ Thu, 08 Oct 2020 20:06:13: 11000000 INFO @ Thu, 08 Oct 2020 20:06:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.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, 08 Oct 2020 20:06:14: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:06:14: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:06:18: 6000000 INFO @ Thu, 08 Oct 2020 20:06:19: 12000000 INFO @ Thu, 08 Oct 2020 20:06:21: 1000000 INFO @ Thu, 08 Oct 2020 20:06:21: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:21: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:21: #1 total tags in treatment: 12299487 INFO @ Thu, 08 Oct 2020 20:06:21: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:06:21: #1 tags after filtering in treatment: 12299487 INFO @ Thu, 08 Oct 2020 20:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:21: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:21: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:22: #2 number of paired peaks: 891 WARNING @ Thu, 08 Oct 2020 20:06:22: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:22: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:22: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:22: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:22: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:22: #2 predicted fragment length is 163 bps INFO @ Thu, 08 Oct 2020 20:06:22: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 08 Oct 2020 20:06:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05_model.r INFO @ Thu, 08 Oct 2020 20:06:22: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:23: 7000000 INFO @ Thu, 08 Oct 2020 20:06:27: 2000000 INFO @ Thu, 08 Oct 2020 20:06:29: 8000000 INFO @ Thu, 08 Oct 2020 20:06:33: 3000000 INFO @ Thu, 08 Oct 2020 20:06:34: 9000000 INFO @ Thu, 08 Oct 2020 20:06:39: 10000000 INFO @ Thu, 08 Oct 2020 20:06:40: 4000000 INFO @ Thu, 08 Oct 2020 20:06:44: 11000000 INFO @ Thu, 08 Oct 2020 20:06:47: 5000000 INFO @ Thu, 08 Oct 2020 20:06:50: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:50: 12000000 INFO @ Thu, 08 Oct 2020 20:06:52: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:52: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:52: #1 total tags in treatment: 12299487 INFO @ Thu, 08 Oct 2020 20:06:52: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:06:52: #1 tags after filtering in treatment: 12299487 INFO @ Thu, 08 Oct 2020 20:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:52: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:52: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:53: #2 number of paired peaks: 891 WARNING @ Thu, 08 Oct 2020 20:06:53: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:53: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:53: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:53: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:53: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:53: #2 predicted fragment length is 163 bps INFO @ Thu, 08 Oct 2020 20:06:53: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 08 Oct 2020 20:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10_model.r INFO @ Thu, 08 Oct 2020 20:06:53: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:54: 6000000 INFO @ Thu, 08 Oct 2020 20:07:01: 7000000 INFO @ Thu, 08 Oct 2020 20:07:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.05_summits.bed INFO @ Thu, 08 Oct 2020 20:07:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7390 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:08: 8000000 INFO @ Thu, 08 Oct 2020 20:07:15: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:07:20: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:22: 10000000 INFO @ Thu, 08 Oct 2020 20:07:30: 11000000 INFO @ Thu, 08 Oct 2020 20:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.10_summits.bed INFO @ Thu, 08 Oct 2020 20:07:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4924 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:37: 12000000 INFO @ Thu, 08 Oct 2020 20:07:39: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:39: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:39: #1 total tags in treatment: 12299487 INFO @ Thu, 08 Oct 2020 20:07:39: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:07:39: #1 tags after filtering in treatment: 12299487 INFO @ Thu, 08 Oct 2020 20:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:39: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:39: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:40: #2 number of paired peaks: 891 WARNING @ Thu, 08 Oct 2020 20:07:40: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Thu, 08 Oct 2020 20:07:40: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:40: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:40: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:40: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:40: #2 predicted fragment length is 163 bps INFO @ Thu, 08 Oct 2020 20:07:40: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 08 Oct 2020 20:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20_model.r INFO @ Thu, 08 Oct 2020 20:07:40: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:08:08: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832069/SRX8832069.20_summits.bed INFO @ Thu, 08 Oct 2020 20:08:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2379 records, 4 fields): 5 millis CompletedMACS2peakCalling