Job ID = 14158922 SRX = SRX8976717 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8727221 spots for SRR12483321/SRR12483321.sra Written 8727221 spots for SRR12483321/SRR12483321.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159265 ("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: 00:09:33 8727221 reads; of these: 8727221 (100.00%) were paired; of these: 2121632 (24.31%) aligned concordantly 0 times 5455604 (62.51%) aligned concordantly exactly 1 time 1149985 (13.18%) aligned concordantly >1 times ---- 2121632 pairs aligned concordantly 0 times; of these: 335799 (15.83%) aligned discordantly 1 time ---- 1785833 pairs aligned 0 times concordantly or discordantly; of these: 3571666 mates make up the pairs; of these: 3324041 (93.07%) aligned 0 times 118121 (3.31%) aligned exactly 1 time 129504 (3.63%) aligned >1 times 80.96% overall alignment rate Time searching: 00:09:33 Overall time: 00:09:33 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] 4053797 / 6938692 = 0.5842 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 18:36:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.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 18:36:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:36:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:37:07: 1000000 INFO @ Wed, 08 Dec 2021 18:37:17: 2000000 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 18:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.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 18:37:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:37:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:37:26: 3000000 INFO @ Wed, 08 Dec 2021 18:37:34: 1000000 INFO @ Wed, 08 Dec 2021 18:37:34: 4000000 INFO @ Wed, 08 Dec 2021 18:37:42: 2000000 INFO @ Wed, 08 Dec 2021 18:37:43: 5000000 INFO @ Wed, 08 Dec 2021 18:37:50: 3000000 INFO @ Wed, 08 Dec 2021 18:37:51: 6000000 INFO @ Wed, 08 Dec 2021 18:37:51: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:37:51: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:37:51: #1 total tags in treatment: 2704575 INFO @ Wed, 08 Dec 2021 18:37:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:37:51: #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 18:37:51: #1 tags after filtering in treatment: 2548170 INFO @ Wed, 08 Dec 2021 18:37:51: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:37:51: #1 finished! INFO @ Wed, 08 Dec 2021 18:37:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:37:52: #2 number of paired peaks: 1069 INFO @ Wed, 08 Dec 2021 18:37:52: start model_add_line... INFO @ Wed, 08 Dec 2021 18:37:52: start X-correlation... INFO @ Wed, 08 Dec 2021 18:37:52: end of X-cor INFO @ Wed, 08 Dec 2021 18:37:52: #2 finished! INFO @ Wed, 08 Dec 2021 18:37:52: #2 predicted fragment length is 176 bps INFO @ Wed, 08 Dec 2021 18:37:52: #2 alternative fragment length(s) may be 4,176 bps INFO @ Wed, 08 Dec 2021 18:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.05_model.r INFO @ Wed, 08 Dec 2021 18:37:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:37:52: #3 Pre-compute pvalue-qvalue table... 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 18:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.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 18:37:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:37:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:37:58: 4000000 INFO @ Wed, 08 Dec 2021 18:38:02: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:38:06: 5000000 INFO @ Wed, 08 Dec 2021 18:38:06: 1000000 INFO @ Wed, 08 Dec 2021 18:38:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:38:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:38:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.05_summits.bed INFO @ Wed, 08 Dec 2021 18:38:07: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (439 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:38:14: 6000000 INFO @ Wed, 08 Dec 2021 18:38:14: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:38:14: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:38:14: #1 total tags in treatment: 2704575 INFO @ Wed, 08 Dec 2021 18:38:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:38:14: #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 18:38:14: #1 tags after filtering in treatment: 2548170 INFO @ Wed, 08 Dec 2021 18:38:14: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:38:14: #1 finished! INFO @ Wed, 08 Dec 2021 18:38:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:38:14: #2 number of paired peaks: 1069 INFO @ Wed, 08 Dec 2021 18:38:14: start model_add_line... INFO @ Wed, 08 Dec 2021 18:38:14: start X-correlation... INFO @ Wed, 08 Dec 2021 18:38:14: end of X-cor INFO @ Wed, 08 Dec 2021 18:38:14: #2 finished! INFO @ Wed, 08 Dec 2021 18:38:14: #2 predicted fragment length is 176 bps INFO @ Wed, 08 Dec 2021 18:38:14: #2 alternative fragment length(s) may be 4,176 bps INFO @ Wed, 08 Dec 2021 18:38:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.10_model.r INFO @ Wed, 08 Dec 2021 18:38:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:38:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:38:17: 2000000 INFO @ Wed, 08 Dec 2021 18:38:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:38:27: 3000000 INFO @ Wed, 08 Dec 2021 18:38:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:38:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:38:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.10_summits.bed INFO @ Wed, 08 Dec 2021 18:38:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:38:37: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:38:48: 5000000 INFO @ Wed, 08 Dec 2021 18:38:58: 6000000 INFO @ Wed, 08 Dec 2021 18:38:58: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:38:58: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:38:58: #1 total tags in treatment: 2704575 INFO @ Wed, 08 Dec 2021 18:38:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:38:58: #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 18:38:58: #1 tags after filtering in treatment: 2548170 INFO @ Wed, 08 Dec 2021 18:38:58: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:38:58: #1 finished! INFO @ Wed, 08 Dec 2021 18:38:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:38:58: #2 number of paired peaks: 1069 INFO @ Wed, 08 Dec 2021 18:38:58: start model_add_line... INFO @ Wed, 08 Dec 2021 18:38:58: start X-correlation... INFO @ Wed, 08 Dec 2021 18:38:58: end of X-cor INFO @ Wed, 08 Dec 2021 18:38:58: #2 finished! INFO @ Wed, 08 Dec 2021 18:38:58: #2 predicted fragment length is 176 bps INFO @ Wed, 08 Dec 2021 18:38:58: #2 alternative fragment length(s) may be 4,176 bps INFO @ Wed, 08 Dec 2021 18:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.20_model.r INFO @ Wed, 08 Dec 2021 18:38:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:38:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:39:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976717/SRX8976717.20_summits.bed INFO @ Wed, 08 Dec 2021 18:39:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 5 millis CompletedMACS2peakCalling