Job ID = 16434288 SRX = SRX10925647 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: 00:04:11 22878026 reads; of these: 22878026 (100.00%) were unpaired; of these: 16465522 (71.97%) aligned 0 times 5211909 (22.78%) aligned exactly 1 time 1200595 (5.25%) aligned >1 times 28.03% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 1013586 / 6412504 = 0.1581 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.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, 02 Aug 2022 09:57:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:57:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:57:28: 1000000 INFO @ Tue, 02 Aug 2022 09:57:34: 2000000 INFO @ Tue, 02 Aug 2022 09:57:39: 3000000 INFO @ Tue, 02 Aug 2022 09:57:45: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:57:50: 5000000 INFO @ Tue, 02 Aug 2022 09:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.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, 02 Aug 2022 09:57:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:57:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:57:53: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:57:53: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:57:53: #1 total tags in treatment: 5398918 INFO @ Tue, 02 Aug 2022 09:57:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:57:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:57:53: #1 tags after filtering in treatment: 5398918 INFO @ Tue, 02 Aug 2022 09:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:57:53: #1 finished! INFO @ Tue, 02 Aug 2022 09:57:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:57:53: #2 number of paired peaks: 4837 INFO @ Tue, 02 Aug 2022 09:57:53: start model_add_line... INFO @ Tue, 02 Aug 2022 09:57:54: start X-correlation... INFO @ Tue, 02 Aug 2022 09:57:54: end of X-cor INFO @ Tue, 02 Aug 2022 09:57:54: #2 finished! INFO @ Tue, 02 Aug 2022 09:57:54: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 09:57:54: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 09:57:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.05_model.r INFO @ Tue, 02 Aug 2022 09:57:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:57:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:57:58: 1000000 INFO @ Tue, 02 Aug 2022 09:58:03: 2000000 INFO @ Tue, 02 Aug 2022 09:58:09: 3000000 INFO @ Tue, 02 Aug 2022 09:58:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:58:15: 4000000 INFO @ Tue, 02 Aug 2022 09:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:58:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.05_summits.bed INFO @ Tue, 02 Aug 2022 09:58:17: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9967 records, 4 fields): 38 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:58:21: 5000000 INFO @ Tue, 02 Aug 2022 09:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.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, 02 Aug 2022 09:58:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:58:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:58:23: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:58:23: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:58:23: #1 total tags in treatment: 5398918 INFO @ Tue, 02 Aug 2022 09:58:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:58:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:58:23: #1 tags after filtering in treatment: 5398918 INFO @ Tue, 02 Aug 2022 09:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:58:23: #1 finished! INFO @ Tue, 02 Aug 2022 09:58:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:58:24: #2 number of paired peaks: 4837 INFO @ Tue, 02 Aug 2022 09:58:24: start model_add_line... INFO @ Tue, 02 Aug 2022 09:58:24: start X-correlation... INFO @ Tue, 02 Aug 2022 09:58:24: end of X-cor INFO @ Tue, 02 Aug 2022 09:58:24: #2 finished! INFO @ Tue, 02 Aug 2022 09:58:24: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 09:58:24: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 09:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.10_model.r INFO @ Tue, 02 Aug 2022 09:58:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:58:27: 1000000 INFO @ Tue, 02 Aug 2022 09:58:33: 2000000 INFO @ Tue, 02 Aug 2022 09:58:38: 3000000 INFO @ Tue, 02 Aug 2022 09:58:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:58:44: 4000000 INFO @ Tue, 02 Aug 2022 09:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:58:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:58:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.10_summits.bed INFO @ Tue, 02 Aug 2022 09:58:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5333 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:58:49: 5000000 INFO @ Tue, 02 Aug 2022 09:58:52: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:58:52: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:58:52: #1 total tags in treatment: 5398918 INFO @ Tue, 02 Aug 2022 09:58:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:58:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:58:52: #1 tags after filtering in treatment: 5398918 INFO @ Tue, 02 Aug 2022 09:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:58:52: #1 finished! INFO @ Tue, 02 Aug 2022 09:58:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:58:53: #2 number of paired peaks: 4837 INFO @ Tue, 02 Aug 2022 09:58:53: start model_add_line... INFO @ Tue, 02 Aug 2022 09:58:53: start X-correlation... INFO @ Tue, 02 Aug 2022 09:58:53: end of X-cor INFO @ Tue, 02 Aug 2022 09:58:53: #2 finished! INFO @ Tue, 02 Aug 2022 09:58:53: #2 predicted fragment length is 234 bps INFO @ Tue, 02 Aug 2022 09:58:53: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 02 Aug 2022 09:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.20_model.r INFO @ Tue, 02 Aug 2022 09:58:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:58:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:59:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:59:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:59:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:59:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10925647/SRX10925647.20_summits.bed INFO @ Tue, 02 Aug 2022 09:59:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2071 records, 4 fields): 16 millis CompletedMACS2peakCalling