Job ID = 16435143 SRX = SRX13110341 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:38:00 prefetch.2.10.7: 1) Downloading 'SRR16918011'... 2022-08-02T01:38:00 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:38:28 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:38:29 prefetch.2.10.7: 'SRR16918011' is valid 2022-08-02T01:38:29 prefetch.2.10.7: 1) 'SRR16918011' was downloaded successfully 2022-08-02T01:38:29 prefetch.2.10.7: 'SRR16918011' has 0 unresolved dependencies Read 16667868 spots for SRR16918011/SRR16918011.sra Written 16667868 spots for SRR16918011/SRR16918011.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435531 ("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: 00:04:17 16667868 reads; of these: 16667868 (100.00%) were unpaired; of these: 2655602 (15.93%) aligned 0 times 12121099 (72.72%) aligned exactly 1 time 1891167 (11.35%) aligned >1 times 84.07% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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] 2495873 / 14012266 = 0.1781 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 10:46:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.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 10:46:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:46:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:47:01: 1000000 INFO @ Tue, 02 Aug 2022 10:47:07: 2000000 INFO @ Tue, 02 Aug 2022 10:47:12: 3000000 INFO @ Tue, 02 Aug 2022 10:47:17: 4000000 INFO @ Tue, 02 Aug 2022 10:47:22: 5000000 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 10:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.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 10:47:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:47:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:47:27: 6000000 INFO @ Tue, 02 Aug 2022 10:47:30: 1000000 INFO @ Tue, 02 Aug 2022 10:47:33: 7000000 INFO @ Tue, 02 Aug 2022 10:47:36: 2000000 INFO @ Tue, 02 Aug 2022 10:47:38: 8000000 INFO @ Tue, 02 Aug 2022 10:47:41: 3000000 INFO @ Tue, 02 Aug 2022 10:47:43: 9000000 INFO @ Tue, 02 Aug 2022 10:47:46: 4000000 INFO @ Tue, 02 Aug 2022 10:47:48: 10000000 INFO @ Tue, 02 Aug 2022 10:47:51: 5000000 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 10:47:54: 11000000 INFO @ Tue, 02 Aug 2022 10:47:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.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 10:47:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:47:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:47:56: 6000000 INFO @ Tue, 02 Aug 2022 10:47:57: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:47:57: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:47:57: #1 total tags in treatment: 11516393 INFO @ Tue, 02 Aug 2022 10:47:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:47:57: #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 10:47:57: #1 tags after filtering in treatment: 11516393 INFO @ Tue, 02 Aug 2022 10:47:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:47:57: #1 finished! INFO @ Tue, 02 Aug 2022 10:47:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:47:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:47:58: #2 number of paired peaks: 1366 INFO @ Tue, 02 Aug 2022 10:47:58: start model_add_line... INFO @ Tue, 02 Aug 2022 10:47:58: start X-correlation... INFO @ Tue, 02 Aug 2022 10:47:58: end of X-cor INFO @ Tue, 02 Aug 2022 10:47:58: #2 finished! INFO @ Tue, 02 Aug 2022 10:47:58: #2 predicted fragment length is 208 bps INFO @ Tue, 02 Aug 2022 10:47:58: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 02 Aug 2022 10:47:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.05_model.r INFO @ Tue, 02 Aug 2022 10:47:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:47:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:48:00: 1000000 INFO @ Tue, 02 Aug 2022 10:48:02: 7000000 INFO @ Tue, 02 Aug 2022 10:48:05: 2000000 INFO @ Tue, 02 Aug 2022 10:48:07: 8000000 INFO @ Tue, 02 Aug 2022 10:48:11: 3000000 INFO @ Tue, 02 Aug 2022 10:48:12: 9000000 INFO @ Tue, 02 Aug 2022 10:48:16: 4000000 INFO @ Tue, 02 Aug 2022 10:48:17: 10000000 INFO @ Tue, 02 Aug 2022 10:48:21: 5000000 INFO @ Tue, 02 Aug 2022 10:48:23: 11000000 INFO @ Tue, 02 Aug 2022 10:48:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:48:26: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:48:26: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:48:26: #1 total tags in treatment: 11516393 INFO @ Tue, 02 Aug 2022 10:48:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:48:26: #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 10:48:26: #1 tags after filtering in treatment: 11516393 INFO @ Tue, 02 Aug 2022 10:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:48:26: #1 finished! INFO @ Tue, 02 Aug 2022 10:48:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:48:26: 6000000 INFO @ Tue, 02 Aug 2022 10:48:27: #2 number of paired peaks: 1366 INFO @ Tue, 02 Aug 2022 10:48:27: start model_add_line... INFO @ Tue, 02 Aug 2022 10:48:27: start X-correlation... INFO @ Tue, 02 Aug 2022 10:48:27: end of X-cor INFO @ Tue, 02 Aug 2022 10:48:27: #2 finished! INFO @ Tue, 02 Aug 2022 10:48:27: #2 predicted fragment length is 208 bps INFO @ Tue, 02 Aug 2022 10:48:27: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 02 Aug 2022 10:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.10_model.r INFO @ Tue, 02 Aug 2022 10:48:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:48:31: 7000000 INFO @ Tue, 02 Aug 2022 10:48:36: 8000000 INFO @ Tue, 02 Aug 2022 10:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.05_summits.bed INFO @ Tue, 02 Aug 2022 10:48:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8947 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:48:41: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:48:46: 10000000 INFO @ Tue, 02 Aug 2022 10:48:51: 11000000 INFO @ Tue, 02 Aug 2022 10:48:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:48:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:48:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:48:53: #1 total tags in treatment: 11516393 INFO @ Tue, 02 Aug 2022 10:48:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:48:53: #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 10:48:54: #1 tags after filtering in treatment: 11516393 INFO @ Tue, 02 Aug 2022 10:48:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:48:54: #1 finished! INFO @ Tue, 02 Aug 2022 10:48:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:48:55: #2 number of paired peaks: 1366 INFO @ Tue, 02 Aug 2022 10:48:55: start model_add_line... INFO @ Tue, 02 Aug 2022 10:48:55: start X-correlation... INFO @ Tue, 02 Aug 2022 10:48:55: end of X-cor INFO @ Tue, 02 Aug 2022 10:48:55: #2 finished! INFO @ Tue, 02 Aug 2022 10:48:55: #2 predicted fragment length is 208 bps INFO @ Tue, 02 Aug 2022 10:48:55: #2 alternative fragment length(s) may be 208 bps INFO @ Tue, 02 Aug 2022 10:48:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.20_model.r INFO @ Tue, 02 Aug 2022 10:48:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.10_summits.bed INFO @ Tue, 02 Aug 2022 10:49:06: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6672 records, 4 fields): 34 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:49:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110341/SRX13110341.20_summits.bed INFO @ Tue, 02 Aug 2022 10:49:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4504 records, 4 fields): 27 millis CompletedMACS2peakCalling