Job ID = 14159661 SRX = SRX8976698 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: 00:12:54 16411894 reads; of these: 16411894 (100.00%) were paired; of these: 2680804 (16.33%) aligned concordantly 0 times 11007638 (67.07%) aligned concordantly exactly 1 time 2723452 (16.59%) aligned concordantly >1 times ---- 2680804 pairs aligned concordantly 0 times; of these: 1693621 (63.18%) aligned discordantly 1 time ---- 987183 pairs aligned 0 times concordantly or discordantly; of these: 1974366 mates make up the pairs; of these: 1026454 (51.99%) aligned 0 times 332066 (16.82%) aligned exactly 1 time 615846 (31.19%) aligned >1 times 96.87% overall alignment rate Time searching: 00:12:54 Overall time: 00:12:54 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] 2498507 / 15417807 = 0.1621 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 @ Thu, 09 Dec 2021 00:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.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 @ Thu, 09 Dec 2021 00:25:50: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:25:50: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:25:55: 1000000 INFO @ Thu, 09 Dec 2021 00:25:59: 2000000 INFO @ Thu, 09 Dec 2021 00:26:03: 3000000 INFO @ Thu, 09 Dec 2021 00:26:07: 4000000 INFO @ Thu, 09 Dec 2021 00:26:12: 5000000 INFO @ Thu, 09 Dec 2021 00:26:16: 6000000 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 00:26:20: 7000000 INFO @ Thu, 09 Dec 2021 00:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.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 00:26:20: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:26:20: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:26:25: 8000000 INFO @ Thu, 09 Dec 2021 00:26:25: 1000000 INFO @ Thu, 09 Dec 2021 00:26:29: 9000000 INFO @ Thu, 09 Dec 2021 00:26:30: 2000000 INFO @ Thu, 09 Dec 2021 00:26:34: 10000000 INFO @ Thu, 09 Dec 2021 00:26:34: 3000000 INFO @ Thu, 09 Dec 2021 00:26:38: 11000000 INFO @ Thu, 09 Dec 2021 00:26:39: 4000000 INFO @ Thu, 09 Dec 2021 00:26:43: 12000000 INFO @ Thu, 09 Dec 2021 00:26:43: 5000000 INFO @ Thu, 09 Dec 2021 00:26:48: 13000000 INFO @ Thu, 09 Dec 2021 00:26:48: 6000000 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 00:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.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 00:26:50: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:26:50: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:26:52: 14000000 INFO @ Thu, 09 Dec 2021 00:26:53: 7000000 INFO @ Thu, 09 Dec 2021 00:26:55: 1000000 INFO @ Thu, 09 Dec 2021 00:26:57: 15000000 INFO @ Thu, 09 Dec 2021 00:26:57: 8000000 INFO @ Thu, 09 Dec 2021 00:27:00: 2000000 INFO @ Thu, 09 Dec 2021 00:27:02: 16000000 INFO @ Thu, 09 Dec 2021 00:27:02: 9000000 INFO @ Thu, 09 Dec 2021 00:27:05: 3000000 INFO @ Thu, 09 Dec 2021 00:27:06: 17000000 INFO @ Thu, 09 Dec 2021 00:27:07: 10000000 INFO @ Thu, 09 Dec 2021 00:27:09: 4000000 INFO @ Thu, 09 Dec 2021 00:27:11: 18000000 INFO @ Thu, 09 Dec 2021 00:27:11: 11000000 INFO @ Thu, 09 Dec 2021 00:27:14: 5000000 INFO @ Thu, 09 Dec 2021 00:27:16: 19000000 INFO @ Thu, 09 Dec 2021 00:27:16: 12000000 INFO @ Thu, 09 Dec 2021 00:27:19: 6000000 INFO @ Thu, 09 Dec 2021 00:27:20: 20000000 INFO @ Thu, 09 Dec 2021 00:27:21: 13000000 INFO @ Thu, 09 Dec 2021 00:27:23: 7000000 INFO @ Thu, 09 Dec 2021 00:27:25: 21000000 INFO @ Thu, 09 Dec 2021 00:27:25: 14000000 INFO @ Thu, 09 Dec 2021 00:27:28: 8000000 INFO @ Thu, 09 Dec 2021 00:27:29: 22000000 INFO @ Thu, 09 Dec 2021 00:27:30: 15000000 INFO @ Thu, 09 Dec 2021 00:27:33: 9000000 INFO @ Thu, 09 Dec 2021 00:27:34: 23000000 INFO @ Thu, 09 Dec 2021 00:27:35: 16000000 INFO @ Thu, 09 Dec 2021 00:27:37: 10000000 INFO @ Thu, 09 Dec 2021 00:27:39: 24000000 INFO @ Thu, 09 Dec 2021 00:27:40: 17000000 INFO @ Thu, 09 Dec 2021 00:27:42: 11000000 INFO @ Thu, 09 Dec 2021 00:27:43: 25000000 INFO @ Thu, 09 Dec 2021 00:27:44: 18000000 INFO @ Thu, 09 Dec 2021 00:27:47: 12000000 INFO @ Thu, 09 Dec 2021 00:27:48: 26000000 INFO @ Thu, 09 Dec 2021 00:27:49: 19000000 INFO @ Thu, 09 Dec 2021 00:27:51: 13000000 INFO @ Thu, 09 Dec 2021 00:27:52: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:27:52: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:27:52: #1 total tags in treatment: 11440199 INFO @ Thu, 09 Dec 2021 00:27:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:27:52: #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 00:27:52: #1 tags after filtering in treatment: 9991793 INFO @ Thu, 09 Dec 2021 00:27:52: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 00:27:52: #1 finished! INFO @ Thu, 09 Dec 2021 00:27:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:27:53: #2 number of paired peaks: 2256 INFO @ Thu, 09 Dec 2021 00:27:53: start model_add_line... INFO @ Thu, 09 Dec 2021 00:27:53: start X-correlation... INFO @ Thu, 09 Dec 2021 00:27:53: end of X-cor INFO @ Thu, 09 Dec 2021 00:27:53: #2 finished! INFO @ Thu, 09 Dec 2021 00:27:53: #2 predicted fragment length is 222 bps INFO @ Thu, 09 Dec 2021 00:27:53: #2 alternative fragment length(s) may be 2,189,222,235 bps INFO @ Thu, 09 Dec 2021 00:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.05_model.r INFO @ Thu, 09 Dec 2021 00:27:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:27:54: 20000000 INFO @ Thu, 09 Dec 2021 00:27:56: 14000000 INFO @ Thu, 09 Dec 2021 00:27:58: 21000000 INFO @ Thu, 09 Dec 2021 00:28:01: 15000000 INFO @ Thu, 09 Dec 2021 00:28:03: 22000000 INFO @ Thu, 09 Dec 2021 00:28:05: 16000000 INFO @ Thu, 09 Dec 2021 00:28:08: 23000000 INFO @ Thu, 09 Dec 2021 00:28:10: 17000000 INFO @ Thu, 09 Dec 2021 00:28:12: 24000000 INFO @ Thu, 09 Dec 2021 00:28:15: 18000000 INFO @ Thu, 09 Dec 2021 00:28:17: 25000000 INFO @ Thu, 09 Dec 2021 00:28:19: 19000000 INFO @ Thu, 09 Dec 2021 00:28:19: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:28:22: 26000000 INFO @ Thu, 09 Dec 2021 00:28:24: 20000000 INFO @ Thu, 09 Dec 2021 00:28:26: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:28:26: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:28:26: #1 total tags in treatment: 11440199 INFO @ Thu, 09 Dec 2021 00:28:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:28:26: #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 00:28:26: #1 tags after filtering in treatment: 9991793 INFO @ Thu, 09 Dec 2021 00:28:26: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 00:28:26: #1 finished! INFO @ Thu, 09 Dec 2021 00:28:26: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:28:27: #2 number of paired peaks: 2256 INFO @ Thu, 09 Dec 2021 00:28:27: start model_add_line... INFO @ Thu, 09 Dec 2021 00:28:27: start X-correlation... INFO @ Thu, 09 Dec 2021 00:28:27: end of X-cor INFO @ Thu, 09 Dec 2021 00:28:27: #2 finished! INFO @ Thu, 09 Dec 2021 00:28:27: #2 predicted fragment length is 222 bps INFO @ Thu, 09 Dec 2021 00:28:27: #2 alternative fragment length(s) may be 2,189,222,235 bps INFO @ Thu, 09 Dec 2021 00:28:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.10_model.r INFO @ Thu, 09 Dec 2021 00:28:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:28:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:28:28: 21000000 INFO @ Thu, 09 Dec 2021 00:28:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:28:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:28:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.05_summits.bed INFO @ Thu, 09 Dec 2021 00:28:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1633 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:28:33: 22000000 INFO @ Thu, 09 Dec 2021 00:28:38: 23000000 INFO @ Thu, 09 Dec 2021 00:28:42: 24000000 INFO @ Thu, 09 Dec 2021 00:28:47: 25000000 INFO @ Thu, 09 Dec 2021 00:28:51: 26000000 INFO @ Thu, 09 Dec 2021 00:28:54: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:28:55: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:28:55: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:28:55: #1 total tags in treatment: 11440199 INFO @ Thu, 09 Dec 2021 00:28:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:28:55: #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 00:28:55: #1 tags after filtering in treatment: 9991793 INFO @ Thu, 09 Dec 2021 00:28:55: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 00:28:55: #1 finished! INFO @ Thu, 09 Dec 2021 00:28:55: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:28:56: #2 number of paired peaks: 2256 INFO @ Thu, 09 Dec 2021 00:28:56: start model_add_line... INFO @ Thu, 09 Dec 2021 00:28:56: start X-correlation... INFO @ Thu, 09 Dec 2021 00:28:56: end of X-cor INFO @ Thu, 09 Dec 2021 00:28:56: #2 finished! INFO @ Thu, 09 Dec 2021 00:28:56: #2 predicted fragment length is 222 bps INFO @ Thu, 09 Dec 2021 00:28:56: #2 alternative fragment length(s) may be 2,189,222,235 bps INFO @ Thu, 09 Dec 2021 00:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.20_model.r INFO @ Thu, 09 Dec 2021 00:28:56: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:29:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:29:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:29:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.10_summits.bed INFO @ Thu, 09 Dec 2021 00:29:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (893 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:29:24: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976698/SRX8976698.20_summits.bed INFO @ Thu, 09 Dec 2021 00:29:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (360 records, 4 fields): 2 millis CompletedMACS2peakCalling