Job ID = 14158974 SRX = SRX8976718 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8609018 spots for SRR12483322/SRR12483322.sra Written 8609018 spots for SRR12483322/SRR12483322.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159274 ("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: 00:06:18 8609018 reads; of these: 8609018 (100.00%) were paired; of these: 2103317 (24.43%) aligned concordantly 0 times 5372857 (62.41%) aligned concordantly exactly 1 time 1132844 (13.16%) aligned concordantly >1 times ---- 2103317 pairs aligned concordantly 0 times; of these: 335183 (15.94%) aligned discordantly 1 time ---- 1768134 pairs aligned 0 times concordantly or discordantly; of these: 3536268 mates make up the pairs; of these: 3274662 (92.60%) aligned 0 times 129484 (3.66%) aligned exactly 1 time 132122 (3.74%) aligned >1 times 80.98% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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_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] 3969873 / 6837763 = 0.5806 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 18:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.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 18:38:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:38:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:38:28: 1000000 INFO @ Wed, 08 Dec 2021 18:38:33: 2000000 INFO @ Wed, 08 Dec 2021 18:38:38: 3000000 INFO @ Wed, 08 Dec 2021 18:38:43: 4000000 INFO @ Wed, 08 Dec 2021 18:38:48: 5000000 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 18:38:53: 6000000 INFO @ Wed, 08 Dec 2021 18:38:53: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:38:53: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:38:53: #1 total tags in treatment: 2687358 INFO @ Wed, 08 Dec 2021 18:38:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:38:53: #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 18:38:53: #1 tags after filtering in treatment: 2534170 INFO @ Wed, 08 Dec 2021 18:38:53: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:38:53: #1 finished! INFO @ Wed, 08 Dec 2021 18:38:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:38:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:38:53: #2 number of paired peaks: 1027 INFO @ Wed, 08 Dec 2021 18:38:53: start model_add_line... INFO @ Wed, 08 Dec 2021 18:38:53: start X-correlation... INFO @ Wed, 08 Dec 2021 18:38:53: end of X-cor INFO @ Wed, 08 Dec 2021 18:38:53: #2 finished! INFO @ Wed, 08 Dec 2021 18:38:53: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 18:38:53: #2 alternative fragment length(s) may be 167,183 bps INFO @ Wed, 08 Dec 2021 18:38:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.05_model.r INFO @ Wed, 08 Dec 2021 18:38:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:38:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.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 18:38:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:38:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:38:58: 1000000 INFO @ Wed, 08 Dec 2021 18:38:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:39:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:39:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:39:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.05_summits.bed INFO @ Wed, 08 Dec 2021 18:39:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (422 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:39:03: 2000000 INFO @ Wed, 08 Dec 2021 18:39:08: 3000000 INFO @ Wed, 08 Dec 2021 18:39:14: 4000000 INFO @ Wed, 08 Dec 2021 18:39:19: 5000000 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 18:39:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.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 18:39:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:39:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:39:24: 6000000 INFO @ Wed, 08 Dec 2021 18:39:24: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:39:24: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:39:24: #1 total tags in treatment: 2687358 INFO @ Wed, 08 Dec 2021 18:39:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:39:24: #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 18:39:24: #1 tags after filtering in treatment: 2534170 INFO @ Wed, 08 Dec 2021 18:39:24: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:39:24: #1 finished! INFO @ Wed, 08 Dec 2021 18:39:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:39:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:39:24: #2 number of paired peaks: 1027 INFO @ Wed, 08 Dec 2021 18:39:24: start model_add_line... INFO @ Wed, 08 Dec 2021 18:39:24: start X-correlation... INFO @ Wed, 08 Dec 2021 18:39:24: end of X-cor INFO @ Wed, 08 Dec 2021 18:39:24: #2 finished! INFO @ Wed, 08 Dec 2021 18:39:24: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 18:39:24: #2 alternative fragment length(s) may be 167,183 bps INFO @ Wed, 08 Dec 2021 18:39:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.10_model.r INFO @ Wed, 08 Dec 2021 18:39:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:39:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:39:27: 1000000 INFO @ Wed, 08 Dec 2021 18:39:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:39:32: 2000000 INFO @ Wed, 08 Dec 2021 18:39:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:39:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:39:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.10_summits.bed INFO @ Wed, 08 Dec 2021 18:39:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (253 records, 4 fields): 443 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:39:36: 3000000 INFO @ Wed, 08 Dec 2021 18:39:40: 4000000 INFO @ Wed, 08 Dec 2021 18:39:44: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:39:48: 6000000 INFO @ Wed, 08 Dec 2021 18:39:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:39:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:39:48: #1 total tags in treatment: 2687358 INFO @ Wed, 08 Dec 2021 18:39:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:39:48: #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 18:39:48: #1 tags after filtering in treatment: 2534170 INFO @ Wed, 08 Dec 2021 18:39:48: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:39:48: #1 finished! INFO @ Wed, 08 Dec 2021 18:39:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:39:49: #2 number of paired peaks: 1027 INFO @ Wed, 08 Dec 2021 18:39:49: start model_add_line... INFO @ Wed, 08 Dec 2021 18:39:49: start X-correlation... INFO @ Wed, 08 Dec 2021 18:39:49: end of X-cor INFO @ Wed, 08 Dec 2021 18:39:49: #2 finished! INFO @ Wed, 08 Dec 2021 18:39:49: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 18:39:49: #2 alternative fragment length(s) may be 167,183 bps INFO @ Wed, 08 Dec 2021 18:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.20_model.r INFO @ Wed, 08 Dec 2021 18:39:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:39:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976718/SRX8976718.20_summits.bed INFO @ Wed, 08 Dec 2021 18:39:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。