Job ID = 14160474 SRX = SRX9555450 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: 00:17:13 25997655 reads; of these: 25997655 (100.00%) were paired; of these: 5136864 (19.76%) aligned concordantly 0 times 18039830 (69.39%) aligned concordantly exactly 1 time 2820961 (10.85%) aligned concordantly >1 times ---- 5136864 pairs aligned concordantly 0 times; of these: 497983 (9.69%) aligned discordantly 1 time ---- 4638881 pairs aligned 0 times concordantly or discordantly; of these: 9277762 mates make up the pairs; of these: 8672117 (93.47%) aligned 0 times 420868 (4.54%) aligned exactly 1 time 184777 (1.99%) aligned >1 times 83.32% overall alignment rate Time searching: 00:17:13 Overall time: 00:17:13 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 20 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] 2382558 / 21301841 = 0.1118 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 03:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.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 03:11:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:11:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:11:15: 1000000 INFO @ Thu, 09 Dec 2021 03:11:20: 2000000 INFO @ Thu, 09 Dec 2021 03:11:25: 3000000 INFO @ Thu, 09 Dec 2021 03:11:30: 4000000 INFO @ Thu, 09 Dec 2021 03:11:35: 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 03:11:40: 6000000 INFO @ Thu, 09 Dec 2021 03:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.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 03:11:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:11:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:11:45: 7000000 INFO @ Thu, 09 Dec 2021 03:11:46: 1000000 INFO @ Thu, 09 Dec 2021 03:11:51: 8000000 INFO @ Thu, 09 Dec 2021 03:11:52: 2000000 INFO @ Thu, 09 Dec 2021 03:11:56: 9000000 INFO @ Thu, 09 Dec 2021 03:11:57: 3000000 INFO @ Thu, 09 Dec 2021 03:12:02: 10000000 INFO @ Thu, 09 Dec 2021 03:12:03: 4000000 INFO @ Thu, 09 Dec 2021 03:12:07: 11000000 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 03:12:09: 5000000 INFO @ Thu, 09 Dec 2021 03:12:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.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 03:12:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:12:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:12:13: 12000000 INFO @ Thu, 09 Dec 2021 03:12:14: 6000000 INFO @ Thu, 09 Dec 2021 03:12:16: 1000000 INFO @ Thu, 09 Dec 2021 03:12:19: 13000000 INFO @ Thu, 09 Dec 2021 03:12:20: 7000000 INFO @ Thu, 09 Dec 2021 03:12:22: 2000000 INFO @ Thu, 09 Dec 2021 03:12:24: 14000000 INFO @ Thu, 09 Dec 2021 03:12:26: 8000000 INFO @ Thu, 09 Dec 2021 03:12:28: 3000000 INFO @ Thu, 09 Dec 2021 03:12:30: 15000000 INFO @ Thu, 09 Dec 2021 03:12:31: 9000000 INFO @ Thu, 09 Dec 2021 03:12:33: 4000000 INFO @ Thu, 09 Dec 2021 03:12:36: 16000000 INFO @ Thu, 09 Dec 2021 03:12:37: 10000000 INFO @ Thu, 09 Dec 2021 03:12:39: 5000000 INFO @ Thu, 09 Dec 2021 03:12:42: 17000000 INFO @ Thu, 09 Dec 2021 03:12:42: 11000000 INFO @ Thu, 09 Dec 2021 03:12:45: 6000000 INFO @ Thu, 09 Dec 2021 03:12:47: 18000000 INFO @ Thu, 09 Dec 2021 03:12:48: 12000000 INFO @ Thu, 09 Dec 2021 03:12:51: 7000000 INFO @ Thu, 09 Dec 2021 03:12:53: 19000000 INFO @ Thu, 09 Dec 2021 03:12:54: 13000000 INFO @ Thu, 09 Dec 2021 03:12:56: 8000000 INFO @ Thu, 09 Dec 2021 03:12:59: 20000000 INFO @ Thu, 09 Dec 2021 03:13:00: 14000000 INFO @ Thu, 09 Dec 2021 03:13:02: 9000000 INFO @ Thu, 09 Dec 2021 03:13:04: 21000000 INFO @ Thu, 09 Dec 2021 03:13:05: 15000000 INFO @ Thu, 09 Dec 2021 03:13:08: 10000000 INFO @ Thu, 09 Dec 2021 03:13:10: 22000000 INFO @ Thu, 09 Dec 2021 03:13:11: 16000000 INFO @ Thu, 09 Dec 2021 03:13:14: 11000000 INFO @ Thu, 09 Dec 2021 03:13:16: 23000000 INFO @ Thu, 09 Dec 2021 03:13:17: 17000000 INFO @ Thu, 09 Dec 2021 03:13:19: 12000000 INFO @ Thu, 09 Dec 2021 03:13:22: 24000000 INFO @ Thu, 09 Dec 2021 03:13:23: 18000000 INFO @ Thu, 09 Dec 2021 03:13:25: 13000000 INFO @ Thu, 09 Dec 2021 03:13:27: 25000000 INFO @ Thu, 09 Dec 2021 03:13:28: 19000000 INFO @ Thu, 09 Dec 2021 03:13:31: 14000000 INFO @ Thu, 09 Dec 2021 03:13:33: 26000000 INFO @ Thu, 09 Dec 2021 03:13:34: 20000000 INFO @ Thu, 09 Dec 2021 03:13:36: 15000000 INFO @ Thu, 09 Dec 2021 03:13:39: 27000000 INFO @ Thu, 09 Dec 2021 03:13:40: 21000000 INFO @ Thu, 09 Dec 2021 03:13:42: 16000000 INFO @ Thu, 09 Dec 2021 03:13:45: 28000000 INFO @ Thu, 09 Dec 2021 03:13:45: 22000000 INFO @ Thu, 09 Dec 2021 03:13:48: 17000000 INFO @ Thu, 09 Dec 2021 03:13:50: 29000000 INFO @ Thu, 09 Dec 2021 03:13:51: 23000000 INFO @ Thu, 09 Dec 2021 03:13:54: 18000000 INFO @ Thu, 09 Dec 2021 03:13:56: 30000000 INFO @ Thu, 09 Dec 2021 03:13:57: 24000000 INFO @ Thu, 09 Dec 2021 03:13:59: 19000000 INFO @ Thu, 09 Dec 2021 03:14:02: 31000000 INFO @ Thu, 09 Dec 2021 03:14:02: 25000000 INFO @ Thu, 09 Dec 2021 03:14:05: 20000000 INFO @ Thu, 09 Dec 2021 03:14:07: 32000000 INFO @ Thu, 09 Dec 2021 03:14:08: 26000000 INFO @ Thu, 09 Dec 2021 03:14:11: 21000000 INFO @ Thu, 09 Dec 2021 03:14:13: 33000000 INFO @ Thu, 09 Dec 2021 03:14:14: 27000000 INFO @ Thu, 09 Dec 2021 03:14:16: 22000000 INFO @ Thu, 09 Dec 2021 03:14:19: 34000000 INFO @ Thu, 09 Dec 2021 03:14:19: 28000000 INFO @ Thu, 09 Dec 2021 03:14:22: 23000000 INFO @ Thu, 09 Dec 2021 03:14:25: 35000000 INFO @ Thu, 09 Dec 2021 03:14:25: 29000000 INFO @ Thu, 09 Dec 2021 03:14:28: 24000000 INFO @ Thu, 09 Dec 2021 03:14:30: 36000000 INFO @ Thu, 09 Dec 2021 03:14:31: 30000000 INFO @ Thu, 09 Dec 2021 03:14:34: 25000000 INFO @ Thu, 09 Dec 2021 03:14:36: 37000000 INFO @ Thu, 09 Dec 2021 03:14:36: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:14:39: 26000000 INFO @ Thu, 09 Dec 2021 03:14:42: 38000000 INFO @ Thu, 09 Dec 2021 03:14:42: 32000000 INFO @ Thu, 09 Dec 2021 03:14:45: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:14:45: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:14:45: #1 total tags in treatment: 18499904 INFO @ Thu, 09 Dec 2021 03:14:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:14:45: #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 03:14:45: 27000000 INFO @ Thu, 09 Dec 2021 03:14:45: #1 tags after filtering in treatment: 16934562 INFO @ Thu, 09 Dec 2021 03:14:45: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 03:14:45: #1 finished! INFO @ Thu, 09 Dec 2021 03:14:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:14:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:14:46: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:14:46: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:14:46: start model_add_line... INFO @ Thu, 09 Dec 2021 03:14:46: start X-correlation... INFO @ Thu, 09 Dec 2021 03:14:46: end of X-cor INFO @ Thu, 09 Dec 2021 03:14:46: #2 finished! INFO @ Thu, 09 Dec 2021 03:14:46: #2 predicted fragment length is 121 bps INFO @ Thu, 09 Dec 2021 03:14:46: #2 alternative fragment length(s) may be 3,108,121 bps INFO @ Thu, 09 Dec 2021 03:14:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.05_model.r INFO @ Thu, 09 Dec 2021 03:14:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:14:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:14:47: 33000000 INFO @ Thu, 09 Dec 2021 03:14:51: 28000000 INFO @ Thu, 09 Dec 2021 03:14:53: 34000000 INFO @ Thu, 09 Dec 2021 03:14:56: 29000000 INFO @ Thu, 09 Dec 2021 03:14:58: 35000000 INFO @ Thu, 09 Dec 2021 03:15:02: 30000000 INFO @ Thu, 09 Dec 2021 03:15:04: 36000000 INFO @ Thu, 09 Dec 2021 03:15:07: 31000000 INFO @ Thu, 09 Dec 2021 03:15:09: 37000000 INFO @ Thu, 09 Dec 2021 03:15:13: 32000000 INFO @ Thu, 09 Dec 2021 03:15:15: 38000000 INFO @ Thu, 09 Dec 2021 03:15:16: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:15:18: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:15:18: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:15:18: #1 total tags in treatment: 18499904 INFO @ Thu, 09 Dec 2021 03:15:18: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:15:18: #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 03:15:18: #1 tags after filtering in treatment: 16934562 INFO @ Thu, 09 Dec 2021 03:15:18: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 03:15:18: #1 finished! INFO @ Thu, 09 Dec 2021 03:15:18: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:15:18: 33000000 INFO @ Thu, 09 Dec 2021 03:15:19: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:15:19: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:15:19: start model_add_line... INFO @ Thu, 09 Dec 2021 03:15:20: start X-correlation... INFO @ Thu, 09 Dec 2021 03:15:20: end of X-cor INFO @ Thu, 09 Dec 2021 03:15:20: #2 finished! INFO @ Thu, 09 Dec 2021 03:15:20: #2 predicted fragment length is 121 bps INFO @ Thu, 09 Dec 2021 03:15:20: #2 alternative fragment length(s) may be 3,108,121 bps INFO @ Thu, 09 Dec 2021 03:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.10_model.r INFO @ Thu, 09 Dec 2021 03:15:20: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:15:24: 34000000 INFO @ Thu, 09 Dec 2021 03:15:29: 35000000 INFO @ Thu, 09 Dec 2021 03:15:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.05_summits.bed INFO @ Thu, 09 Dec 2021 03:15:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (451 records, 4 fields): 81 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:15:34: 36000000 INFO @ Thu, 09 Dec 2021 03:15:39: 37000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:15:45: 38000000 INFO @ Thu, 09 Dec 2021 03:15:48: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:15:48: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:15:48: #1 total tags in treatment: 18499904 INFO @ Thu, 09 Dec 2021 03:15:48: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:15:48: #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 03:15:48: #1 tags after filtering in treatment: 16934562 INFO @ Thu, 09 Dec 2021 03:15:48: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 03:15:48: #1 finished! INFO @ Thu, 09 Dec 2021 03:15:48: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:15:49: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:15:49: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 03:15:49: start model_add_line... INFO @ Thu, 09 Dec 2021 03:15:49: start X-correlation... INFO @ Thu, 09 Dec 2021 03:15:49: end of X-cor INFO @ Thu, 09 Dec 2021 03:15:49: #2 finished! INFO @ Thu, 09 Dec 2021 03:15:49: #2 predicted fragment length is 121 bps INFO @ Thu, 09 Dec 2021 03:15:49: #2 alternative fragment length(s) may be 3,108,121 bps INFO @ Thu, 09 Dec 2021 03:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.20_model.r INFO @ Thu, 09 Dec 2021 03:15:49: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:15:49: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.10_summits.bed INFO @ Thu, 09 Dec 2021 03:16:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (332 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:16:19: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555450/SRX9555450.20_summits.bed INFO @ Thu, 09 Dec 2021 03:16:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling