Job ID = 14159683 SRX = SRX8832111 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11077363 spots for SRR12332035/SRR12332035.sra Written 11077363 spots for SRR12332035/SRR12332035.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160289 ("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: 00:02:17 11077363 reads; of these: 11077363 (100.00%) were unpaired; of these: 2206417 (19.92%) aligned 0 times 7244380 (65.40%) aligned exactly 1 time 1626566 (14.68%) aligned >1 times 80.08% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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_rmdupse_core] 3072058 / 8870946 = 0.3463 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.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, 09 Dec 2021 00:25:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:25:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:25:20: 1000000 INFO @ Thu, 09 Dec 2021 00:25:25: 2000000 INFO @ Thu, 09 Dec 2021 00:25:29: 3000000 INFO @ Thu, 09 Dec 2021 00:25:34: 4000000 INFO @ Thu, 09 Dec 2021 00:25:39: 5000000 INFO @ Thu, 09 Dec 2021 00:25:42: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:25:42: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:25:42: #1 total tags in treatment: 5798888 INFO @ Thu, 09 Dec 2021 00:25:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:25:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:25:43: #1 tags after filtering in treatment: 5798888 INFO @ Thu, 09 Dec 2021 00:25:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:25:43: #1 finished! INFO @ Thu, 09 Dec 2021 00:25:43: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:25:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:25:43: #2 number of paired peaks: 2639 INFO @ Thu, 09 Dec 2021 00:25:43: start model_add_line... INFO @ Thu, 09 Dec 2021 00:25:43: start X-correlation... INFO @ Thu, 09 Dec 2021 00:25:43: end of X-cor INFO @ Thu, 09 Dec 2021 00:25:43: #2 finished! INFO @ Thu, 09 Dec 2021 00:25:43: #2 predicted fragment length is 155 bps INFO @ Thu, 09 Dec 2021 00:25:43: #2 alternative fragment length(s) may be 155 bps INFO @ Thu, 09 Dec 2021 00:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.05_model.r INFO @ Thu, 09 Dec 2021 00:25:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:25:43: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.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, 09 Dec 2021 00:25:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:25:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:25:50: 1000000 INFO @ Thu, 09 Dec 2021 00:25:55: 2000000 INFO @ Thu, 09 Dec 2021 00:25:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:26:00: 3000000 INFO @ Thu, 09 Dec 2021 00:26:04: 4000000 INFO @ Thu, 09 Dec 2021 00:26:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.05_summits.bed INFO @ Thu, 09 Dec 2021 00:26:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6797 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:26:09: 5000000 INFO @ Thu, 09 Dec 2021 00:26:13: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:26:13: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:26:13: #1 total tags in treatment: 5798888 INFO @ Thu, 09 Dec 2021 00:26:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:26:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:26:13: #1 tags after filtering in treatment: 5798888 INFO @ Thu, 09 Dec 2021 00:26:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:26:13: #1 finished! INFO @ Thu, 09 Dec 2021 00:26:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:26:13: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:26:14: #2 number of paired peaks: 2639 INFO @ Thu, 09 Dec 2021 00:26:14: start model_add_line... INFO @ Thu, 09 Dec 2021 00:26:14: start X-correlation... INFO @ Thu, 09 Dec 2021 00:26:14: end of X-cor INFO @ Thu, 09 Dec 2021 00:26:14: #2 finished! INFO @ Thu, 09 Dec 2021 00:26:14: #2 predicted fragment length is 155 bps INFO @ Thu, 09 Dec 2021 00:26:14: #2 alternative fragment length(s) may be 155 bps INFO @ Thu, 09 Dec 2021 00:26:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.10_model.r INFO @ Thu, 09 Dec 2021 00:26:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:26:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:26:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.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, 09 Dec 2021 00:26:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:26:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:26:20: 1000000 INFO @ Thu, 09 Dec 2021 00:26:24: 2000000 INFO @ Thu, 09 Dec 2021 00:26:28: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:26:29: 3000000 INFO @ Thu, 09 Dec 2021 00:26:34: 4000000 INFO @ Thu, 09 Dec 2021 00:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.10_summits.bed INFO @ Thu, 09 Dec 2021 00:26:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5116 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:26:39: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:26:42: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 00:26:42: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 00:26:42: #1 total tags in treatment: 5798888 INFO @ Thu, 09 Dec 2021 00:26:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:26:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:26:42: #1 tags after filtering in treatment: 5798888 INFO @ Thu, 09 Dec 2021 00:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:26:42: #1 finished! INFO @ Thu, 09 Dec 2021 00:26:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:26:43: #2 number of paired peaks: 2639 INFO @ Thu, 09 Dec 2021 00:26:43: start model_add_line... INFO @ Thu, 09 Dec 2021 00:26:43: start X-correlation... INFO @ Thu, 09 Dec 2021 00:26:43: end of X-cor INFO @ Thu, 09 Dec 2021 00:26:43: #2 finished! INFO @ Thu, 09 Dec 2021 00:26:43: #2 predicted fragment length is 155 bps INFO @ Thu, 09 Dec 2021 00:26:43: #2 alternative fragment length(s) may be 155 bps INFO @ Thu, 09 Dec 2021 00:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.20_model.r INFO @ Thu, 09 Dec 2021 00:26:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:26:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:26:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:27:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:27:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:27:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832111/SRX8832111.20_summits.bed INFO @ Thu, 09 Dec 2021 00:27:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3594 records, 4 fields): 5 millis CompletedMACS2peakCalling