Job ID = 14159633 SRX = SRX8976694 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: 00:15:41 14040347 reads; of these: 14040347 (100.00%) were paired; of these: 2195639 (15.64%) aligned concordantly 0 times 9636356 (68.63%) aligned concordantly exactly 1 time 2208352 (15.73%) aligned concordantly >1 times ---- 2195639 pairs aligned concordantly 0 times; of these: 1320169 (60.13%) aligned discordantly 1 time ---- 875470 pairs aligned 0 times concordantly or discordantly; of these: 1750940 mates make up the pairs; of these: 1024247 (58.50%) aligned 0 times 264295 (15.09%) aligned exactly 1 time 462398 (26.41%) aligned >1 times 96.35% overall alignment rate Time searching: 00:15:41 Overall time: 00:15:41 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 12 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] 2599201 / 13159373 = 0.1975 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 23:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.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 23:59:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:59:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:59:42: 1000000 INFO @ Wed, 08 Dec 2021 23:59:49: 2000000 INFO @ Wed, 08 Dec 2021 23:59:56: 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 @ Thu, 09 Dec 2021 00:00:03: 4000000 INFO @ Thu, 09 Dec 2021 00:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.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 00:00:05: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:00:05: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:00:10: 5000000 INFO @ Thu, 09 Dec 2021 00:00:14: 1000000 INFO @ Thu, 09 Dec 2021 00:00:17: 6000000 INFO @ Thu, 09 Dec 2021 00:00:22: 2000000 INFO @ Thu, 09 Dec 2021 00:00:24: 7000000 INFO @ Thu, 09 Dec 2021 00:00:30: 3000000 INFO @ Thu, 09 Dec 2021 00:00:31: 8000000 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 00:00:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.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 00:00:35: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:00:35: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:00:38: 9000000 INFO @ Thu, 09 Dec 2021 00:00:38: 4000000 INFO @ Thu, 09 Dec 2021 00:00:45: 1000000 INFO @ Thu, 09 Dec 2021 00:00:46: 10000000 INFO @ Thu, 09 Dec 2021 00:00:47: 5000000 INFO @ Thu, 09 Dec 2021 00:00:53: 11000000 INFO @ Thu, 09 Dec 2021 00:00:54: 2000000 INFO @ Thu, 09 Dec 2021 00:00:55: 6000000 INFO @ Thu, 09 Dec 2021 00:01:00: 12000000 INFO @ Thu, 09 Dec 2021 00:01:03: 3000000 INFO @ Thu, 09 Dec 2021 00:01:03: 7000000 INFO @ Thu, 09 Dec 2021 00:01:07: 13000000 INFO @ Thu, 09 Dec 2021 00:01:11: 4000000 INFO @ Thu, 09 Dec 2021 00:01:12: 8000000 INFO @ Thu, 09 Dec 2021 00:01:14: 14000000 INFO @ Thu, 09 Dec 2021 00:01:19: 5000000 INFO @ Thu, 09 Dec 2021 00:01:21: 15000000 INFO @ Thu, 09 Dec 2021 00:01:21: 9000000 INFO @ Thu, 09 Dec 2021 00:01:28: 6000000 INFO @ Thu, 09 Dec 2021 00:01:28: 16000000 INFO @ Thu, 09 Dec 2021 00:01:30: 10000000 INFO @ Thu, 09 Dec 2021 00:01:35: 17000000 INFO @ Thu, 09 Dec 2021 00:01:37: 7000000 INFO @ Thu, 09 Dec 2021 00:01:39: 11000000 INFO @ Thu, 09 Dec 2021 00:01:42: 18000000 INFO @ Thu, 09 Dec 2021 00:01:45: 8000000 INFO @ Thu, 09 Dec 2021 00:01:48: 12000000 INFO @ Thu, 09 Dec 2021 00:01:49: 19000000 INFO @ Thu, 09 Dec 2021 00:01:55: 9000000 INFO @ Thu, 09 Dec 2021 00:01:56: 20000000 INFO @ Thu, 09 Dec 2021 00:01:57: 13000000 INFO @ Thu, 09 Dec 2021 00:02:03: 21000000 INFO @ Thu, 09 Dec 2021 00:02:03: 10000000 INFO @ Thu, 09 Dec 2021 00:02:05: 14000000 INFO @ Thu, 09 Dec 2021 00:02:09: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:02:09: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:02:09: #1 total tags in treatment: 9444942 INFO @ Thu, 09 Dec 2021 00:02:09: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:02:09: #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 00:02:09: #1 tags after filtering in treatment: 8471869 INFO @ Thu, 09 Dec 2021 00:02:09: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 00:02:09: #1 finished! INFO @ Thu, 09 Dec 2021 00:02:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:02:10: #2 number of paired peaks: 1854 INFO @ Thu, 09 Dec 2021 00:02:10: start model_add_line... INFO @ Thu, 09 Dec 2021 00:02:10: start X-correlation... INFO @ Thu, 09 Dec 2021 00:02:10: end of X-cor INFO @ Thu, 09 Dec 2021 00:02:10: #2 finished! INFO @ Thu, 09 Dec 2021 00:02:10: #2 predicted fragment length is 213 bps INFO @ Thu, 09 Dec 2021 00:02:10: #2 alternative fragment length(s) may be 2,193,213,232 bps INFO @ Thu, 09 Dec 2021 00:02:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.05_model.r INFO @ Thu, 09 Dec 2021 00:02:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:02:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:02:12: 11000000 INFO @ Thu, 09 Dec 2021 00:02:13: 15000000 INFO @ Thu, 09 Dec 2021 00:02:20: 12000000 INFO @ Thu, 09 Dec 2021 00:02:21: 16000000 INFO @ Thu, 09 Dec 2021 00:02:29: 13000000 INFO @ Thu, 09 Dec 2021 00:02:29: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:02:38: 18000000 INFO @ Thu, 09 Dec 2021 00:02:38: 14000000 INFO @ Thu, 09 Dec 2021 00:02:41: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:02:47: 19000000 INFO @ Thu, 09 Dec 2021 00:02:47: 15000000 INFO @ Thu, 09 Dec 2021 00:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.05_summits.bed INFO @ Thu, 09 Dec 2021 00:02:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1226 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:02:55: 16000000 INFO @ Thu, 09 Dec 2021 00:02:56: 20000000 INFO @ Thu, 09 Dec 2021 00:03:04: 21000000 INFO @ Thu, 09 Dec 2021 00:03:04: 17000000 INFO @ Thu, 09 Dec 2021 00:03:10: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:03:10: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:03:10: #1 total tags in treatment: 9444942 INFO @ Thu, 09 Dec 2021 00:03:10: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:03:10: #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 00:03:11: #1 tags after filtering in treatment: 8471869 INFO @ Thu, 09 Dec 2021 00:03:11: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 00:03:11: #1 finished! INFO @ Thu, 09 Dec 2021 00:03:11: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:03:12: #2 number of paired peaks: 1854 INFO @ Thu, 09 Dec 2021 00:03:12: start model_add_line... INFO @ Thu, 09 Dec 2021 00:03:12: start X-correlation... INFO @ Thu, 09 Dec 2021 00:03:12: end of X-cor INFO @ Thu, 09 Dec 2021 00:03:12: #2 finished! INFO @ Thu, 09 Dec 2021 00:03:12: #2 predicted fragment length is 213 bps INFO @ Thu, 09 Dec 2021 00:03:12: #2 alternative fragment length(s) may be 2,193,213,232 bps INFO @ Thu, 09 Dec 2021 00:03:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.10_model.r INFO @ Thu, 09 Dec 2021 00:03:12: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:03:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:03:12: 18000000 INFO @ Thu, 09 Dec 2021 00:03:21: 19000000 INFO @ Thu, 09 Dec 2021 00:03:29: 20000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:03:37: 21000000 INFO @ Thu, 09 Dec 2021 00:03:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:03:44: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:03:44: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:03:44: #1 total tags in treatment: 9444942 INFO @ Thu, 09 Dec 2021 00:03:44: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:03:44: #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 00:03:44: #1 tags after filtering in treatment: 8471869 INFO @ Thu, 09 Dec 2021 00:03:44: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 00:03:44: #1 finished! INFO @ Thu, 09 Dec 2021 00:03:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:03:45: #2 number of paired peaks: 1854 INFO @ Thu, 09 Dec 2021 00:03:45: start model_add_line... INFO @ Thu, 09 Dec 2021 00:03:45: start X-correlation... INFO @ Thu, 09 Dec 2021 00:03:45: end of X-cor INFO @ Thu, 09 Dec 2021 00:03:45: #2 finished! INFO @ Thu, 09 Dec 2021 00:03:45: #2 predicted fragment length is 213 bps INFO @ Thu, 09 Dec 2021 00:03:45: #2 alternative fragment length(s) may be 2,193,213,232 bps INFO @ Thu, 09 Dec 2021 00:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.20_model.r INFO @ Thu, 09 Dec 2021 00:03:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:03:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:03:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:03:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.10_summits.bed INFO @ Thu, 09 Dec 2021 00:03:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (642 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:04:16: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976694/SRX8976694.20_summits.bed INFO @ Thu, 09 Dec 2021 00:04:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 3 millis CompletedMACS2peakCalling