Job ID = 14159167 SRX = SRX8976706 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: 00:18:38 13112146 reads; of these: 13112146 (100.00%) were paired; of these: 2189184 (16.70%) aligned concordantly 0 times 8663447 (66.07%) aligned concordantly exactly 1 time 2259515 (17.23%) aligned concordantly >1 times ---- 2189184 pairs aligned concordantly 0 times; of these: 1474407 (67.35%) aligned discordantly 1 time ---- 714777 pairs aligned 0 times concordantly or discordantly; of these: 1429554 mates make up the pairs; of these: 453430 (31.72%) aligned 0 times 390899 (27.34%) aligned exactly 1 time 585225 (40.94%) aligned >1 times 98.27% overall alignment rate Time searching: 00:18:38 Overall time: 00:18:38 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] 3353344 / 12390888 = 0.2706 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 20:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.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 20:26:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:26:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:26:54: 1000000 INFO @ Wed, 08 Dec 2021 20:27:02: 2000000 INFO @ Wed, 08 Dec 2021 20:27:09: 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 20:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.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 20:27:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:27:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:27:17: 4000000 INFO @ Wed, 08 Dec 2021 20:27:25: 1000000 INFO @ Wed, 08 Dec 2021 20:27:27: 5000000 INFO @ Wed, 08 Dec 2021 20:27:33: 2000000 INFO @ Wed, 08 Dec 2021 20:27:37: 6000000 INFO @ Wed, 08 Dec 2021 20:27:41: 3000000 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 20:27:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.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 20:27:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:27:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:27:46: 7000000 INFO @ Wed, 08 Dec 2021 20:27:50: 4000000 INFO @ Wed, 08 Dec 2021 20:27:55: 1000000 INFO @ Wed, 08 Dec 2021 20:27:56: 8000000 INFO @ Wed, 08 Dec 2021 20:27:59: 5000000 INFO @ Wed, 08 Dec 2021 20:28:05: 2000000 INFO @ Wed, 08 Dec 2021 20:28:05: 9000000 INFO @ Wed, 08 Dec 2021 20:28:09: 6000000 INFO @ Wed, 08 Dec 2021 20:28:14: 10000000 INFO @ Wed, 08 Dec 2021 20:28:15: 3000000 INFO @ Wed, 08 Dec 2021 20:28:17: 7000000 INFO @ Wed, 08 Dec 2021 20:28:24: 11000000 INFO @ Wed, 08 Dec 2021 20:28:25: 4000000 INFO @ Wed, 08 Dec 2021 20:28:26: 8000000 INFO @ Wed, 08 Dec 2021 20:28:34: 9000000 INFO @ Wed, 08 Dec 2021 20:28:34: 5000000 INFO @ Wed, 08 Dec 2021 20:28:34: 12000000 INFO @ Wed, 08 Dec 2021 20:28:43: 10000000 INFO @ Wed, 08 Dec 2021 20:28:43: 6000000 INFO @ Wed, 08 Dec 2021 20:28:45: 13000000 INFO @ Wed, 08 Dec 2021 20:28:52: 11000000 INFO @ Wed, 08 Dec 2021 20:28:53: 7000000 INFO @ Wed, 08 Dec 2021 20:28:55: 14000000 INFO @ Wed, 08 Dec 2021 20:29:01: 12000000 INFO @ Wed, 08 Dec 2021 20:29:02: 8000000 INFO @ Wed, 08 Dec 2021 20:29:04: 15000000 INFO @ Wed, 08 Dec 2021 20:29:10: 13000000 INFO @ Wed, 08 Dec 2021 20:29:11: 9000000 INFO @ Wed, 08 Dec 2021 20:29:14: 16000000 INFO @ Wed, 08 Dec 2021 20:29:19: 14000000 INFO @ Wed, 08 Dec 2021 20:29:20: 10000000 INFO @ Wed, 08 Dec 2021 20:29:24: 17000000 INFO @ Wed, 08 Dec 2021 20:29:28: 15000000 INFO @ Wed, 08 Dec 2021 20:29:29: 11000000 INFO @ Wed, 08 Dec 2021 20:29:34: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:29:37: 16000000 INFO @ Wed, 08 Dec 2021 20:29:39: 12000000 INFO @ Wed, 08 Dec 2021 20:29:44: 19000000 INFO @ Wed, 08 Dec 2021 20:29:44: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:29:44: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:29:44: #1 total tags in treatment: 7867236 INFO @ Wed, 08 Dec 2021 20:29:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:29:44: #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 20:29:44: #1 tags after filtering in treatment: 7026902 INFO @ Wed, 08 Dec 2021 20:29:44: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:29:44: #1 finished! INFO @ Wed, 08 Dec 2021 20:29:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:29:45: #2 number of paired peaks: 748 WARNING @ Wed, 08 Dec 2021 20:29:45: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Wed, 08 Dec 2021 20:29:45: start model_add_line... INFO @ Wed, 08 Dec 2021 20:29:45: start X-correlation... INFO @ Wed, 08 Dec 2021 20:29:45: end of X-cor INFO @ Wed, 08 Dec 2021 20:29:45: #2 finished! INFO @ Wed, 08 Dec 2021 20:29:45: #2 predicted fragment length is 161 bps INFO @ Wed, 08 Dec 2021 20:29:45: #2 alternative fragment length(s) may be 4,161 bps INFO @ Wed, 08 Dec 2021 20:29:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.05_model.r INFO @ Wed, 08 Dec 2021 20:29:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:29:46: 17000000 INFO @ Wed, 08 Dec 2021 20:29:48: 13000000 INFO @ Wed, 08 Dec 2021 20:29:54: 18000000 INFO @ Wed, 08 Dec 2021 20:29:58: 14000000 INFO @ Wed, 08 Dec 2021 20:30:03: 19000000 INFO @ Wed, 08 Dec 2021 20:30:03: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:30:03: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:30:03: #1 total tags in treatment: 7867236 INFO @ Wed, 08 Dec 2021 20:30:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:30:03: #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 20:30:04: #1 tags after filtering in treatment: 7026902 INFO @ Wed, 08 Dec 2021 20:30:04: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:30:04: #1 finished! INFO @ Wed, 08 Dec 2021 20:30:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:30:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:30:04: #2 number of paired peaks: 748 WARNING @ Wed, 08 Dec 2021 20:30:04: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Wed, 08 Dec 2021 20:30:04: start model_add_line... INFO @ Wed, 08 Dec 2021 20:30:04: start X-correlation... INFO @ Wed, 08 Dec 2021 20:30:04: end of X-cor INFO @ Wed, 08 Dec 2021 20:30:04: #2 finished! INFO @ Wed, 08 Dec 2021 20:30:04: #2 predicted fragment length is 161 bps INFO @ Wed, 08 Dec 2021 20:30:04: #2 alternative fragment length(s) may be 4,161 bps INFO @ Wed, 08 Dec 2021 20:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.10_model.r INFO @ Wed, 08 Dec 2021 20:30:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:30:08: 15000000 INFO @ Wed, 08 Dec 2021 20:30:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:30:17: 16000000 INFO @ Wed, 08 Dec 2021 20:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.05_summits.bed INFO @ Wed, 08 Dec 2021 20:30:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (825 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:30:27: 17000000 INFO @ Wed, 08 Dec 2021 20:30:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:30:36: 18000000 INFO @ Wed, 08 Dec 2021 20:30:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:30:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:30:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.10_summits.bed INFO @ Wed, 08 Dec 2021 20:30:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:30:45: 19000000 INFO @ Wed, 08 Dec 2021 20:30:46: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:30:46: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:30:46: #1 total tags in treatment: 7867236 INFO @ Wed, 08 Dec 2021 20:30:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:30:46: #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 20:30:46: #1 tags after filtering in treatment: 7026902 INFO @ Wed, 08 Dec 2021 20:30:46: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:30:46: #1 finished! INFO @ Wed, 08 Dec 2021 20:30:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:30:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:30:47: #2 number of paired peaks: 748 WARNING @ Wed, 08 Dec 2021 20:30:47: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Wed, 08 Dec 2021 20:30:47: start model_add_line... INFO @ Wed, 08 Dec 2021 20:30:47: start X-correlation... INFO @ Wed, 08 Dec 2021 20:30:47: end of X-cor INFO @ Wed, 08 Dec 2021 20:30:47: #2 finished! INFO @ Wed, 08 Dec 2021 20:30:47: #2 predicted fragment length is 161 bps INFO @ Wed, 08 Dec 2021 20:30:47: #2 alternative fragment length(s) may be 4,161 bps INFO @ Wed, 08 Dec 2021 20:30:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.20_model.r INFO @ Wed, 08 Dec 2021 20:30:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:30:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:31:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:31:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:31:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:31:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976706/SRX8976706.20_summits.bed INFO @ Wed, 08 Dec 2021 20:31:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 3 millis CompletedMACS2peakCalling