Job ID = 16436084 SRX = SRX13110346 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: 00:03:31 11741156 reads; of these: 11741156 (100.00%) were unpaired; of these: 1912030 (16.28%) aligned 0 times 8555810 (72.87%) aligned exactly 1 time 1273316 (10.84%) aligned >1 times 83.72% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 1876311 / 9829126 = 0.1909 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 10:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.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 10:59:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:59:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:59:44: 1000000 INFO @ Tue, 02 Aug 2022 10:59:50: 2000000 INFO @ Tue, 02 Aug 2022 10:59:57: 3000000 INFO @ Tue, 02 Aug 2022 11:00:03: 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 11:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.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 11:00:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:11: 5000000 INFO @ Tue, 02 Aug 2022 11:00:15: 1000000 INFO @ Tue, 02 Aug 2022 11:00:19: 6000000 INFO @ Tue, 02 Aug 2022 11:00:23: 2000000 INFO @ Tue, 02 Aug 2022 11:00:27: 7000000 INFO @ Tue, 02 Aug 2022 11:00:31: 3000000 INFO @ Tue, 02 Aug 2022 11:00:34: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:00:34: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:00:34: #1 total tags in treatment: 7952815 INFO @ Tue, 02 Aug 2022 11:00:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:00:34: #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 11:00:34: #1 tags after filtering in treatment: 7952815 INFO @ Tue, 02 Aug 2022 11:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:00:34: #1 finished! INFO @ Tue, 02 Aug 2022 11:00:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:00:35: #2 number of paired peaks: 1480 INFO @ Tue, 02 Aug 2022 11:00:35: start model_add_line... INFO @ Tue, 02 Aug 2022 11:00:35: start X-correlation... INFO @ Tue, 02 Aug 2022 11:00:35: end of X-cor INFO @ Tue, 02 Aug 2022 11:00:35: #2 finished! INFO @ Tue, 02 Aug 2022 11:00:35: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 11:00:35: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 11:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.05_model.r INFO @ Tue, 02 Aug 2022 11:00:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:00:35: #3 Pre-compute pvalue-qvalue table... 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 11:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.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 11:00:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:39: 4000000 INFO @ Tue, 02 Aug 2022 11:00:45: 1000000 INFO @ Tue, 02 Aug 2022 11:00:47: 5000000 INFO @ Tue, 02 Aug 2022 11:00:54: 2000000 INFO @ Tue, 02 Aug 2022 11:00:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:00:55: 6000000 INFO @ Tue, 02 Aug 2022 11:01:02: 3000000 INFO @ Tue, 02 Aug 2022 11:01:03: 7000000 INFO @ Tue, 02 Aug 2022 11:01:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:01:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:01:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.05_summits.bed INFO @ Tue, 02 Aug 2022 11:01:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7028 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:01:10: 4000000 INFO @ Tue, 02 Aug 2022 11:01:11: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:01:11: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:01:11: #1 total tags in treatment: 7952815 INFO @ Tue, 02 Aug 2022 11:01:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:01:11: #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 11:01:11: #1 tags after filtering in treatment: 7952815 INFO @ Tue, 02 Aug 2022 11:01:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:01:11: #1 finished! INFO @ Tue, 02 Aug 2022 11:01:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:01:11: #2 number of paired peaks: 1480 INFO @ Tue, 02 Aug 2022 11:01:11: start model_add_line... INFO @ Tue, 02 Aug 2022 11:01:11: start X-correlation... INFO @ Tue, 02 Aug 2022 11:01:11: end of X-cor INFO @ Tue, 02 Aug 2022 11:01:11: #2 finished! INFO @ Tue, 02 Aug 2022 11:01:11: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 11:01:11: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 11:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.10_model.r INFO @ Tue, 02 Aug 2022 11:01:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:01:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:01:16: 5000000 INFO @ Tue, 02 Aug 2022 11:01:23: 6000000 INFO @ Tue, 02 Aug 2022 11:01:29: 7000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:01:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:01:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:01:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:01:35: #1 total tags in treatment: 7952815 INFO @ Tue, 02 Aug 2022 11:01:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:01:35: #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 11:01:35: #1 tags after filtering in treatment: 7952815 INFO @ Tue, 02 Aug 2022 11:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:01:35: #1 finished! INFO @ Tue, 02 Aug 2022 11:01:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:01:36: #2 number of paired peaks: 1480 INFO @ Tue, 02 Aug 2022 11:01:36: start model_add_line... INFO @ Tue, 02 Aug 2022 11:01:36: start X-correlation... INFO @ Tue, 02 Aug 2022 11:01:36: end of X-cor INFO @ Tue, 02 Aug 2022 11:01:36: #2 finished! INFO @ Tue, 02 Aug 2022 11:01:36: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 11:01:36: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 11:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.20_model.r INFO @ Tue, 02 Aug 2022 11:01:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:01:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:01:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:01:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.10_summits.bed INFO @ Tue, 02 Aug 2022 11:01:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4821 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:01:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:02:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:02:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:02:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110346/SRX13110346.20_summits.bed INFO @ Tue, 02 Aug 2022 11:02:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2767 records, 4 fields): 5 millis CompletedMACS2peakCalling