Job ID = 14159274 SRX = SRX8976718 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:55 8609018 reads; of these: 8609018 (100.00%) were paired; of these: 2103282 (24.43%) aligned concordantly 0 times 5372834 (62.41%) aligned concordantly exactly 1 time 1132902 (13.16%) aligned concordantly >1 times ---- 2103282 pairs aligned concordantly 0 times; of these: 335211 (15.94%) aligned discordantly 1 time ---- 1768071 pairs aligned 0 times concordantly or discordantly; of these: 3536142 mates make up the pairs; of these: 3274542 (92.60%) aligned 0 times 129472 (3.66%) aligned exactly 1 time 132128 (3.74%) aligned >1 times 80.98% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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] 3969938 / 6837824 = 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 20:47:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 20:47:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:47:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:47:42: 1000000 INFO @ Wed, 08 Dec 2021 20:47:50: 2000000 INFO @ Wed, 08 Dec 2021 20:47:58: 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 20:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 20:48:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:48:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:48:05: 4000000 INFO @ Wed, 08 Dec 2021 20:48:11: 1000000 INFO @ Wed, 08 Dec 2021 20:48:13: 5000000 INFO @ Wed, 08 Dec 2021 20:48:18: 2000000 INFO @ Wed, 08 Dec 2021 20:48:20: 6000000 INFO @ Wed, 08 Dec 2021 20:48:20: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:48:20: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:48:20: #1 total tags in treatment: 2687349 INFO @ Wed, 08 Dec 2021 20:48:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:48:20: #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 20:48:20: #1 tags after filtering in treatment: 2534167 INFO @ Wed, 08 Dec 2021 20:48:20: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:48:20: #1 finished! INFO @ Wed, 08 Dec 2021 20:48:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:48:21: #2 number of paired peaks: 1024 INFO @ Wed, 08 Dec 2021 20:48:21: start model_add_line... INFO @ Wed, 08 Dec 2021 20:48:21: start X-correlation... INFO @ Wed, 08 Dec 2021 20:48:21: end of X-cor INFO @ Wed, 08 Dec 2021 20:48:21: #2 finished! INFO @ Wed, 08 Dec 2021 20:48:21: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 20:48:21: #2 alternative fragment length(s) may be 167 bps INFO @ Wed, 08 Dec 2021 20:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.05_model.r INFO @ Wed, 08 Dec 2021 20:48:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:48:25: 3000000 INFO @ Wed, 08 Dec 2021 20:48:30: #3 Call peaks for each chromosome... 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 20:48:32: 4000000 INFO @ Wed, 08 Dec 2021 20:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.05_summits.bed INFO @ Wed, 08 Dec 2021 20:48:34: Done! INFO @ Wed, 08 Dec 2021 20:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 20:48:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:48:34: #1 read treatment tags... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:48:39: 5000000 INFO @ Wed, 08 Dec 2021 20:48:40: 1000000 INFO @ Wed, 08 Dec 2021 20:48:45: 6000000 INFO @ Wed, 08 Dec 2021 20:48:45: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:48:45: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:48:45: #1 total tags in treatment: 2687349 INFO @ Wed, 08 Dec 2021 20:48:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:48:45: #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 20:48:45: #1 tags after filtering in treatment: 2534167 INFO @ Wed, 08 Dec 2021 20:48:45: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:48:45: #1 finished! INFO @ Wed, 08 Dec 2021 20:48:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:48:46: #2 number of paired peaks: 1024 INFO @ Wed, 08 Dec 2021 20:48:46: start model_add_line... INFO @ Wed, 08 Dec 2021 20:48:46: start X-correlation... INFO @ Wed, 08 Dec 2021 20:48:46: end of X-cor INFO @ Wed, 08 Dec 2021 20:48:46: #2 finished! INFO @ Wed, 08 Dec 2021 20:48:46: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 20:48:46: #2 alternative fragment length(s) may be 167 bps INFO @ Wed, 08 Dec 2021 20:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.10_model.r INFO @ Wed, 08 Dec 2021 20:48:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:48:48: 2000000 INFO @ Wed, 08 Dec 2021 20:48:55: 3000000 INFO @ Wed, 08 Dec 2021 20:48:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.10_summits.bed INFO @ Wed, 08 Dec 2021 20:48:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:49:01: 4000000 INFO @ Wed, 08 Dec 2021 20:49:08: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:49:15: 6000000 INFO @ Wed, 08 Dec 2021 20:49:15: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:49:15: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:49:15: #1 total tags in treatment: 2687349 INFO @ Wed, 08 Dec 2021 20:49:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:49:15: #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 20:49:15: #1 tags after filtering in treatment: 2534167 INFO @ Wed, 08 Dec 2021 20:49:15: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:49:15: #1 finished! INFO @ Wed, 08 Dec 2021 20:49:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:49:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:49:15: #2 number of paired peaks: 1024 INFO @ Wed, 08 Dec 2021 20:49:15: start model_add_line... INFO @ Wed, 08 Dec 2021 20:49:15: start X-correlation... INFO @ Wed, 08 Dec 2021 20:49:15: end of X-cor INFO @ Wed, 08 Dec 2021 20:49:15: #2 finished! INFO @ Wed, 08 Dec 2021 20:49:15: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 20:49:15: #2 alternative fragment length(s) may be 167 bps INFO @ Wed, 08 Dec 2021 20:49:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.20_model.r INFO @ Wed, 08 Dec 2021 20:49:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:49:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:49:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976718/SRX8976718.20_summits.bed INFO @ Wed, 08 Dec 2021 20:49:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 1 millis CompletedMACS2peakCalling