Job ID = 16432190 SRX = SRX15407768 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:31:55 prefetch.2.10.7: 1) Downloading 'SRR19348983'... 2022-08-02T00:31:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:32:20 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:32:21 prefetch.2.10.7: 'SRR19348983' is valid 2022-08-02T00:32:21 prefetch.2.10.7: 1) 'SRR19348983' was downloaded successfully 2022-08-02T00:32:21 prefetch.2.10.7: 'SRR19348983' has 0 unresolved dependencies Read 9758566 spots for SRR19348983/SRR19348983.sra Written 9758566 spots for SRR19348983/SRR19348983.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433129 ("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: 00:01:41 9758566 reads; of these: 9758566 (100.00%) were unpaired; of these: 6285383 (64.41%) aligned 0 times 3058787 (31.34%) aligned exactly 1 time 414396 (4.25%) aligned >1 times 35.59% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 692077 / 3473183 = 0.1993 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 09:35:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.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 09:35:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:35:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:36:00: 1000000 INFO @ Tue, 02 Aug 2022 09:36:06: 2000000 INFO @ Tue, 02 Aug 2022 09:36:11: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:36:11: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:36:11: #1 total tags in treatment: 2781106 INFO @ Tue, 02 Aug 2022 09:36:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:36:11: #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 09:36:11: #1 tags after filtering in treatment: 2781106 INFO @ Tue, 02 Aug 2022 09:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:36:11: #1 finished! INFO @ Tue, 02 Aug 2022 09:36:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:36:11: #2 number of paired peaks: 1623 INFO @ Tue, 02 Aug 2022 09:36:11: start model_add_line... INFO @ Tue, 02 Aug 2022 09:36:11: start X-correlation... INFO @ Tue, 02 Aug 2022 09:36:12: end of X-cor INFO @ Tue, 02 Aug 2022 09:36:12: #2 finished! INFO @ Tue, 02 Aug 2022 09:36:12: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 09:36:12: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 02 Aug 2022 09:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.05_model.r INFO @ Tue, 02 Aug 2022 09:36:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:36:18: #3 Call peaks for each chromosome... 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 09:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.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 09:36:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:36:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:36:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:36:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:36:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.05_summits.bed INFO @ Tue, 02 Aug 2022 09:36:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3713 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:36:27: 1000000 INFO @ Tue, 02 Aug 2022 09:36:33: 2000000 INFO @ Tue, 02 Aug 2022 09:36:38: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:36:38: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:36:38: #1 total tags in treatment: 2781106 INFO @ Tue, 02 Aug 2022 09:36:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:36:38: #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 09:36:38: #1 tags after filtering in treatment: 2781106 INFO @ Tue, 02 Aug 2022 09:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:36:38: #1 finished! INFO @ Tue, 02 Aug 2022 09:36:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:36:38: #2 number of paired peaks: 1623 INFO @ Tue, 02 Aug 2022 09:36:38: start model_add_line... INFO @ Tue, 02 Aug 2022 09:36:38: start X-correlation... INFO @ Tue, 02 Aug 2022 09:36:38: end of X-cor INFO @ Tue, 02 Aug 2022 09:36:38: #2 finished! INFO @ Tue, 02 Aug 2022 09:36:38: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 09:36:38: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 02 Aug 2022 09:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.10_model.r INFO @ Tue, 02 Aug 2022 09:36:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:36:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:36:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.10_summits.bed INFO @ Tue, 02 Aug 2022 09:36:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2291 records, 4 fields): 21 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 09:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.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 09:36:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:36:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:36:58: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:37:04: 2000000 INFO @ Tue, 02 Aug 2022 09:37:09: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:37:09: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:37:09: #1 total tags in treatment: 2781106 INFO @ Tue, 02 Aug 2022 09:37:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:37:09: #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 09:37:09: #1 tags after filtering in treatment: 2781106 INFO @ Tue, 02 Aug 2022 09:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:37:09: #1 finished! INFO @ Tue, 02 Aug 2022 09:37:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:37:09: #2 number of paired peaks: 1623 INFO @ Tue, 02 Aug 2022 09:37:09: start model_add_line... INFO @ Tue, 02 Aug 2022 09:37:09: start X-correlation... INFO @ Tue, 02 Aug 2022 09:37:09: end of X-cor INFO @ Tue, 02 Aug 2022 09:37:09: #2 finished! INFO @ Tue, 02 Aug 2022 09:37:09: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 09:37:09: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 02 Aug 2022 09:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.20_model.r INFO @ Tue, 02 Aug 2022 09:37:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:37:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:37:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407768/SRX15407768.20_summits.bed INFO @ Tue, 02 Aug 2022 09:37:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1012 records, 4 fields): 18 millis CompletedMACS2peakCalling