Job ID = 14159660 SRX = SRX8976697 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: 00:12:25 15231745 reads; of these: 15231745 (100.00%) were paired; of these: 2616371 (17.18%) aligned concordantly 0 times 10109106 (66.37%) aligned concordantly exactly 1 time 2506268 (16.45%) aligned concordantly >1 times ---- 2616371 pairs aligned concordantly 0 times; of these: 1680739 (64.24%) aligned discordantly 1 time ---- 935632 pairs aligned 0 times concordantly or discordantly; of these: 1871264 mates make up the pairs; of these: 963409 (51.48%) aligned 0 times 299876 (16.03%) aligned exactly 1 time 607979 (32.49%) aligned >1 times 96.84% overall alignment rate Time searching: 00:12:25 Overall time: 00:12:25 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] 2159542 / 14289410 = 0.1511 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 00:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.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 00:24:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:24:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:24:18: 1000000 INFO @ Thu, 09 Dec 2021 00:24:23: 2000000 INFO @ Thu, 09 Dec 2021 00:24:28: 3000000 INFO @ Thu, 09 Dec 2021 00:24:34: 4000000 INFO @ Thu, 09 Dec 2021 00:24:39: 5000000 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 00:24:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.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 00:24:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:24:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:24:44: 6000000 INFO @ Thu, 09 Dec 2021 00:24:48: 1000000 INFO @ Thu, 09 Dec 2021 00:24:50: 7000000 INFO @ Thu, 09 Dec 2021 00:24:53: 2000000 INFO @ Thu, 09 Dec 2021 00:24:55: 8000000 INFO @ Thu, 09 Dec 2021 00:24:57: 3000000 INFO @ Thu, 09 Dec 2021 00:25:01: 9000000 INFO @ Thu, 09 Dec 2021 00:25:02: 4000000 INFO @ Thu, 09 Dec 2021 00:25:07: 10000000 INFO @ Thu, 09 Dec 2021 00:25:07: 5000000 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 00:25:12: 6000000 INFO @ Thu, 09 Dec 2021 00:25:12: 11000000 INFO @ Thu, 09 Dec 2021 00:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.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 00:25:12: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:25:12: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:25:16: 7000000 INFO @ Thu, 09 Dec 2021 00:25:17: 1000000 INFO @ Thu, 09 Dec 2021 00:25:18: 12000000 INFO @ Thu, 09 Dec 2021 00:25:21: 8000000 INFO @ Thu, 09 Dec 2021 00:25:22: 2000000 INFO @ Thu, 09 Dec 2021 00:25:23: 13000000 INFO @ Thu, 09 Dec 2021 00:25:26: 9000000 INFO @ Thu, 09 Dec 2021 00:25:27: 3000000 INFO @ Thu, 09 Dec 2021 00:25:29: 14000000 INFO @ Thu, 09 Dec 2021 00:25:31: 10000000 INFO @ Thu, 09 Dec 2021 00:25:32: 4000000 INFO @ Thu, 09 Dec 2021 00:25:35: 15000000 INFO @ Thu, 09 Dec 2021 00:25:36: 11000000 INFO @ Thu, 09 Dec 2021 00:25:36: 5000000 INFO @ Thu, 09 Dec 2021 00:25:40: 16000000 INFO @ Thu, 09 Dec 2021 00:25:40: 12000000 INFO @ Thu, 09 Dec 2021 00:25:41: 6000000 INFO @ Thu, 09 Dec 2021 00:25:45: 13000000 INFO @ Thu, 09 Dec 2021 00:25:46: 17000000 INFO @ Thu, 09 Dec 2021 00:25:46: 7000000 INFO @ Thu, 09 Dec 2021 00:25:50: 14000000 INFO @ Thu, 09 Dec 2021 00:25:51: 8000000 INFO @ Thu, 09 Dec 2021 00:25:51: 18000000 INFO @ Thu, 09 Dec 2021 00:25:55: 15000000 INFO @ Thu, 09 Dec 2021 00:25:56: 9000000 INFO @ Thu, 09 Dec 2021 00:25:57: 19000000 INFO @ Thu, 09 Dec 2021 00:26:00: 16000000 INFO @ Thu, 09 Dec 2021 00:26:00: 10000000 INFO @ Thu, 09 Dec 2021 00:26:02: 20000000 INFO @ Thu, 09 Dec 2021 00:26:04: 17000000 INFO @ Thu, 09 Dec 2021 00:26:05: 11000000 INFO @ Thu, 09 Dec 2021 00:26:08: 21000000 INFO @ Thu, 09 Dec 2021 00:26:09: 18000000 INFO @ Thu, 09 Dec 2021 00:26:10: 12000000 INFO @ Thu, 09 Dec 2021 00:26:14: 22000000 INFO @ Thu, 09 Dec 2021 00:26:14: 19000000 INFO @ Thu, 09 Dec 2021 00:26:15: 13000000 INFO @ Thu, 09 Dec 2021 00:26:19: 20000000 INFO @ Thu, 09 Dec 2021 00:26:19: 23000000 INFO @ Thu, 09 Dec 2021 00:26:19: 14000000 INFO @ Thu, 09 Dec 2021 00:26:24: 21000000 INFO @ Thu, 09 Dec 2021 00:26:24: 15000000 INFO @ Thu, 09 Dec 2021 00:26:25: 24000000 INFO @ Thu, 09 Dec 2021 00:26:29: 22000000 INFO @ Thu, 09 Dec 2021 00:26:29: 16000000 INFO @ Thu, 09 Dec 2021 00:26:30: 25000000 INFO @ Thu, 09 Dec 2021 00:26:31: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:26:31: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:26:31: #1 total tags in treatment: 10653804 INFO @ Thu, 09 Dec 2021 00:26:31: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:26:31: #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 00:26:31: #1 tags after filtering in treatment: 9361518 INFO @ Thu, 09 Dec 2021 00:26:31: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:26:31: #1 finished! INFO @ Thu, 09 Dec 2021 00:26:31: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:26:32: #2 number of paired peaks: 2310 INFO @ Thu, 09 Dec 2021 00:26:32: start model_add_line... INFO @ Thu, 09 Dec 2021 00:26:32: start X-correlation... INFO @ Thu, 09 Dec 2021 00:26:32: end of X-cor INFO @ Thu, 09 Dec 2021 00:26:32: #2 finished! INFO @ Thu, 09 Dec 2021 00:26:32: #2 predicted fragment length is 228 bps INFO @ Thu, 09 Dec 2021 00:26:32: #2 alternative fragment length(s) may be 2,193,228 bps INFO @ Thu, 09 Dec 2021 00:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.05_model.r INFO @ Thu, 09 Dec 2021 00:26:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:26:34: 23000000 INFO @ Thu, 09 Dec 2021 00:26:34: 17000000 INFO @ Thu, 09 Dec 2021 00:26:38: 24000000 INFO @ Thu, 09 Dec 2021 00:26:38: 18000000 INFO @ Thu, 09 Dec 2021 00:26:43: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:26:43: 19000000 INFO @ Thu, 09 Dec 2021 00:26:44: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:26:44: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:26:44: #1 total tags in treatment: 10653804 INFO @ Thu, 09 Dec 2021 00:26:44: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:26:44: #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 00:26:44: #1 tags after filtering in treatment: 9361518 INFO @ Thu, 09 Dec 2021 00:26:44: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:26:44: #1 finished! INFO @ Thu, 09 Dec 2021 00:26:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:26:45: #2 number of paired peaks: 2310 INFO @ Thu, 09 Dec 2021 00:26:45: start model_add_line... INFO @ Thu, 09 Dec 2021 00:26:45: start X-correlation... INFO @ Thu, 09 Dec 2021 00:26:45: end of X-cor INFO @ Thu, 09 Dec 2021 00:26:45: #2 finished! INFO @ Thu, 09 Dec 2021 00:26:45: #2 predicted fragment length is 228 bps INFO @ Thu, 09 Dec 2021 00:26:45: #2 alternative fragment length(s) may be 2,193,228 bps INFO @ Thu, 09 Dec 2021 00:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.10_model.r INFO @ Thu, 09 Dec 2021 00:26:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:26:48: 20000000 INFO @ Thu, 09 Dec 2021 00:26:52: 21000000 INFO @ Thu, 09 Dec 2021 00:26:57: 22000000 INFO @ Thu, 09 Dec 2021 00:26:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:27:01: 23000000 INFO @ Thu, 09 Dec 2021 00:27:05: 24000000 INFO @ Thu, 09 Dec 2021 00:27:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:27:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:27:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.05_summits.bed INFO @ Thu, 09 Dec 2021 00:27:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1584 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:27:09: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:27:10: 25000000 INFO @ Thu, 09 Dec 2021 00:27:11: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:27:11: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:27:11: #1 total tags in treatment: 10653804 INFO @ Thu, 09 Dec 2021 00:27:11: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:27:11: #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 00:27:11: #1 tags after filtering in treatment: 9361518 INFO @ Thu, 09 Dec 2021 00:27:11: #1 Redundant rate of treatment: 0.12 INFO @ Thu, 09 Dec 2021 00:27:11: #1 finished! INFO @ Thu, 09 Dec 2021 00:27:11: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:27:12: #2 number of paired peaks: 2310 INFO @ Thu, 09 Dec 2021 00:27:12: start model_add_line... INFO @ Thu, 09 Dec 2021 00:27:12: start X-correlation... INFO @ Thu, 09 Dec 2021 00:27:12: end of X-cor INFO @ Thu, 09 Dec 2021 00:27:12: #2 finished! INFO @ Thu, 09 Dec 2021 00:27:12: #2 predicted fragment length is 228 bps INFO @ Thu, 09 Dec 2021 00:27:12: #2 alternative fragment length(s) may be 2,193,228 bps INFO @ Thu, 09 Dec 2021 00:27:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.20_model.r INFO @ Thu, 09 Dec 2021 00:27:12: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.10_summits.bed INFO @ Thu, 09 Dec 2021 00:27:19: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (859 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:27:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976697/SRX8976697.20_summits.bed INFO @ Thu, 09 Dec 2021 00:27:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (364 records, 4 fields): 1 millis CompletedMACS2peakCalling