Job ID = 14159549 SRX = SRX8845645 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29668815 spots for SRR12345952/SRR12345952.sra Written 29668815 spots for SRR12345952/SRR12345952.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159940 ("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: 00:32:07 29668815 reads; of these: 29668815 (100.00%) were paired; of these: 17196547 (57.96%) aligned concordantly 0 times 10762872 (36.28%) aligned concordantly exactly 1 time 1709396 (5.76%) aligned concordantly >1 times ---- 17196547 pairs aligned concordantly 0 times; of these: 1668632 (9.70%) aligned discordantly 1 time ---- 15527915 pairs aligned 0 times concordantly or discordantly; of these: 31055830 mates make up the pairs; of these: 29972340 (96.51%) aligned 0 times 332173 (1.07%) aligned exactly 1 time 751317 (2.42%) aligned >1 times 49.49% overall alignment rate Time searching: 00:32:07 Overall time: 00:32:07 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 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 3574301 / 14090227 = 0.2537 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 @ Wed, 08 Dec 2021 23:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.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 @ Wed, 08 Dec 2021 23:07:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:07:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:07:27: 1000000 INFO @ Wed, 08 Dec 2021 23:07:34: 2000000 INFO @ Wed, 08 Dec 2021 23:07:42: 3000000 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 @ Wed, 08 Dec 2021 23:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.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 @ Wed, 08 Dec 2021 23:07:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:07:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:07:49: 4000000 INFO @ Wed, 08 Dec 2021 23:07:57: 1000000 INFO @ Wed, 08 Dec 2021 23:07:57: 5000000 INFO @ Wed, 08 Dec 2021 23:08:05: 2000000 INFO @ Wed, 08 Dec 2021 23:08:05: 6000000 INFO @ Wed, 08 Dec 2021 23:08:13: 3000000 INFO @ Wed, 08 Dec 2021 23:08:13: 7000000 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 @ Wed, 08 Dec 2021 23:08:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.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 @ Wed, 08 Dec 2021 23:08:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:08:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:08:21: 4000000 INFO @ Wed, 08 Dec 2021 23:08:22: 8000000 INFO @ Wed, 08 Dec 2021 23:08:31: 5000000 INFO @ Wed, 08 Dec 2021 23:08:32: 9000000 INFO @ Wed, 08 Dec 2021 23:08:32: 1000000 INFO @ Wed, 08 Dec 2021 23:08:41: 6000000 INFO @ Wed, 08 Dec 2021 23:08:42: 10000000 INFO @ Wed, 08 Dec 2021 23:08:44: 2000000 INFO @ Wed, 08 Dec 2021 23:08:52: 7000000 INFO @ Wed, 08 Dec 2021 23:08:52: 11000000 INFO @ Wed, 08 Dec 2021 23:08:55: 3000000 INFO @ Wed, 08 Dec 2021 23:09:02: 8000000 INFO @ Wed, 08 Dec 2021 23:09:02: 12000000 INFO @ Wed, 08 Dec 2021 23:09:06: 4000000 INFO @ Wed, 08 Dec 2021 23:09:12: 9000000 INFO @ Wed, 08 Dec 2021 23:09:12: 13000000 INFO @ Wed, 08 Dec 2021 23:09:18: 5000000 INFO @ Wed, 08 Dec 2021 23:09:22: 10000000 INFO @ Wed, 08 Dec 2021 23:09:22: 14000000 INFO @ Wed, 08 Dec 2021 23:09:29: 6000000 INFO @ Wed, 08 Dec 2021 23:09:32: 11000000 INFO @ Wed, 08 Dec 2021 23:09:33: 15000000 INFO @ Wed, 08 Dec 2021 23:09:41: 7000000 INFO @ Wed, 08 Dec 2021 23:09:43: 12000000 INFO @ Wed, 08 Dec 2021 23:09:43: 16000000 INFO @ Wed, 08 Dec 2021 23:09:52: 8000000 INFO @ Wed, 08 Dec 2021 23:09:53: 13000000 INFO @ Wed, 08 Dec 2021 23:09:53: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:10:03: 14000000 INFO @ Wed, 08 Dec 2021 23:10:03: 18000000 INFO @ Wed, 08 Dec 2021 23:10:04: 9000000 INFO @ Wed, 08 Dec 2021 23:10:13: 15000000 INFO @ Wed, 08 Dec 2021 23:10:13: 19000000 INFO @ Wed, 08 Dec 2021 23:10:15: 10000000 INFO @ Wed, 08 Dec 2021 23:10:23: 16000000 INFO @ Wed, 08 Dec 2021 23:10:23: 20000000 INFO @ Wed, 08 Dec 2021 23:10:27: 11000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:10:33: 17000000 INFO @ Wed, 08 Dec 2021 23:10:33: 21000000 INFO @ Wed, 08 Dec 2021 23:10:38: 12000000 INFO @ Wed, 08 Dec 2021 23:10:43: 18000000 INFO @ Wed, 08 Dec 2021 23:10:43: 22000000 INFO @ Wed, 08 Dec 2021 23:10:45: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:10:45: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:10:45: #1 total tags in treatment: 9283993 INFO @ Wed, 08 Dec 2021 23:10:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:10:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:10:45: #1 tags after filtering in treatment: 6444848 INFO @ Wed, 08 Dec 2021 23:10:45: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:10:45: #1 finished! INFO @ Wed, 08 Dec 2021 23:10:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:10:46: #2 number of paired peaks: 1571 INFO @ Wed, 08 Dec 2021 23:10:46: start model_add_line... INFO @ Wed, 08 Dec 2021 23:10:46: start X-correlation... INFO @ Wed, 08 Dec 2021 23:10:46: end of X-cor INFO @ Wed, 08 Dec 2021 23:10:46: #2 finished! INFO @ Wed, 08 Dec 2021 23:10:46: #2 predicted fragment length is 262 bps INFO @ Wed, 08 Dec 2021 23:10:46: #2 alternative fragment length(s) may be 262 bps INFO @ Wed, 08 Dec 2021 23:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.05_model.r INFO @ Wed, 08 Dec 2021 23:10:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:10:50: 13000000 INFO @ Wed, 08 Dec 2021 23:10:53: 19000000 INFO @ Wed, 08 Dec 2021 23:11:02: 14000000 INFO @ Wed, 08 Dec 2021 23:11:03: 20000000 INFO @ Wed, 08 Dec 2021 23:11:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.05_summits.bed INFO @ Wed, 08 Dec 2021 23:11:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6668 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:11:13: 21000000 INFO @ Wed, 08 Dec 2021 23:11:13: 15000000 INFO @ Wed, 08 Dec 2021 23:11:23: 22000000 INFO @ Wed, 08 Dec 2021 23:11:25: 16000000 INFO @ Wed, 08 Dec 2021 23:11:25: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:11:25: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:11:25: #1 total tags in treatment: 9283993 INFO @ Wed, 08 Dec 2021 23:11:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:11:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:11:25: #1 tags after filtering in treatment: 6444848 INFO @ Wed, 08 Dec 2021 23:11:25: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:11:25: #1 finished! INFO @ Wed, 08 Dec 2021 23:11:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:11:26: #2 number of paired peaks: 1571 INFO @ Wed, 08 Dec 2021 23:11:26: start model_add_line... INFO @ Wed, 08 Dec 2021 23:11:26: start X-correlation... INFO @ Wed, 08 Dec 2021 23:11:26: end of X-cor INFO @ Wed, 08 Dec 2021 23:11:26: #2 finished! INFO @ Wed, 08 Dec 2021 23:11:26: #2 predicted fragment length is 262 bps INFO @ Wed, 08 Dec 2021 23:11:26: #2 alternative fragment length(s) may be 262 bps INFO @ Wed, 08 Dec 2021 23:11:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.10_model.r INFO @ Wed, 08 Dec 2021 23:11:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:11:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:11:35: 17000000 INFO @ Wed, 08 Dec 2021 23:11:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:11:45: 18000000 INFO @ Wed, 08 Dec 2021 23:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.10_summits.bed INFO @ Wed, 08 Dec 2021 23:11:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4225 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:11:55: 19000000 INFO @ Wed, 08 Dec 2021 23:12:05: 20000000 INFO @ Wed, 08 Dec 2021 23:12:15: 21000000 INFO @ Wed, 08 Dec 2021 23:12:25: 22000000 INFO @ Wed, 08 Dec 2021 23:12:27: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:12:27: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:12:27: #1 total tags in treatment: 9283993 INFO @ Wed, 08 Dec 2021 23:12:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:12:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:12:27: #1 tags after filtering in treatment: 6444848 INFO @ Wed, 08 Dec 2021 23:12:27: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:12:27: #1 finished! INFO @ Wed, 08 Dec 2021 23:12:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:12:28: #2 number of paired peaks: 1571 INFO @ Wed, 08 Dec 2021 23:12:28: start model_add_line... INFO @ Wed, 08 Dec 2021 23:12:28: start X-correlation... INFO @ Wed, 08 Dec 2021 23:12:28: end of X-cor INFO @ Wed, 08 Dec 2021 23:12:28: #2 finished! INFO @ Wed, 08 Dec 2021 23:12:28: #2 predicted fragment length is 262 bps INFO @ Wed, 08 Dec 2021 23:12:28: #2 alternative fragment length(s) may be 262 bps INFO @ Wed, 08 Dec 2021 23:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.20_model.r INFO @ Wed, 08 Dec 2021 23:12:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:12:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845645/SRX8845645.20_summits.bed INFO @ Wed, 08 Dec 2021 23:12:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1942 records, 4 fields): 3 millis CompletedMACS2peakCalling