Job ID = 14160476 SRX = SRX9555459 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: 00:18:37 23289161 reads; of these: 23289161 (100.00%) were paired; of these: 1865435 (8.01%) aligned concordantly 0 times 18618217 (79.94%) aligned concordantly exactly 1 time 2805509 (12.05%) aligned concordantly >1 times ---- 1865435 pairs aligned concordantly 0 times; of these: 613031 (32.86%) aligned discordantly 1 time ---- 1252404 pairs aligned 0 times concordantly or discordantly; of these: 2504808 mates make up the pairs; of these: 1948003 (77.77%) aligned 0 times 372262 (14.86%) aligned exactly 1 time 184543 (7.37%) aligned >1 times 95.82% overall alignment rate Time searching: 00:18:37 Overall time: 00:18:37 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] 2887840 / 22025607 = 0.1311 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 03:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.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 03:13:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:13:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:13:07: 1000000 INFO @ Thu, 09 Dec 2021 03:13:12: 2000000 INFO @ Thu, 09 Dec 2021 03:13:17: 3000000 INFO @ Thu, 09 Dec 2021 03:13:22: 4000000 INFO @ Thu, 09 Dec 2021 03:13:27: 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 03:13:32: 6000000 INFO @ Thu, 09 Dec 2021 03:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.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 03:13:32: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:13:32: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:13:38: 7000000 INFO @ Thu, 09 Dec 2021 03:13:38: 1000000 INFO @ Thu, 09 Dec 2021 03:13:43: 8000000 INFO @ Thu, 09 Dec 2021 03:13:43: 2000000 INFO @ Thu, 09 Dec 2021 03:13:48: 9000000 INFO @ Thu, 09 Dec 2021 03:13:48: 3000000 INFO @ Thu, 09 Dec 2021 03:13:54: 4000000 INFO @ Thu, 09 Dec 2021 03:13:54: 10000000 INFO @ Thu, 09 Dec 2021 03:13:59: 5000000 INFO @ Thu, 09 Dec 2021 03:13:59: 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 03:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.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 03:14:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:14:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:14:05: 6000000 INFO @ Thu, 09 Dec 2021 03:14:05: 12000000 INFO @ Thu, 09 Dec 2021 03:14:08: 1000000 INFO @ Thu, 09 Dec 2021 03:14:10: 7000000 INFO @ Thu, 09 Dec 2021 03:14:10: 13000000 INFO @ Thu, 09 Dec 2021 03:14:14: 2000000 INFO @ Thu, 09 Dec 2021 03:14:16: 8000000 INFO @ Thu, 09 Dec 2021 03:14:16: 14000000 INFO @ Thu, 09 Dec 2021 03:14:19: 3000000 INFO @ Thu, 09 Dec 2021 03:14:21: 15000000 INFO @ Thu, 09 Dec 2021 03:14:21: 9000000 INFO @ Thu, 09 Dec 2021 03:14:25: 4000000 INFO @ Thu, 09 Dec 2021 03:14:27: 16000000 INFO @ Thu, 09 Dec 2021 03:14:27: 10000000 INFO @ Thu, 09 Dec 2021 03:14:30: 5000000 INFO @ Thu, 09 Dec 2021 03:14:32: 17000000 INFO @ Thu, 09 Dec 2021 03:14:32: 11000000 INFO @ Thu, 09 Dec 2021 03:14:36: 6000000 INFO @ Thu, 09 Dec 2021 03:14:38: 18000000 INFO @ Thu, 09 Dec 2021 03:14:38: 12000000 INFO @ Thu, 09 Dec 2021 03:14:41: 7000000 INFO @ Thu, 09 Dec 2021 03:14:43: 19000000 INFO @ Thu, 09 Dec 2021 03:14:43: 13000000 INFO @ Thu, 09 Dec 2021 03:14:46: 8000000 INFO @ Thu, 09 Dec 2021 03:14:48: 20000000 INFO @ Thu, 09 Dec 2021 03:14:48: 14000000 INFO @ Thu, 09 Dec 2021 03:14:52: 9000000 INFO @ Thu, 09 Dec 2021 03:14:53: 21000000 INFO @ Thu, 09 Dec 2021 03:14:54: 15000000 INFO @ Thu, 09 Dec 2021 03:14:57: 10000000 INFO @ Thu, 09 Dec 2021 03:14:59: 22000000 INFO @ Thu, 09 Dec 2021 03:14:59: 16000000 INFO @ Thu, 09 Dec 2021 03:15:02: 11000000 INFO @ Thu, 09 Dec 2021 03:15:04: 23000000 INFO @ Thu, 09 Dec 2021 03:15:05: 17000000 INFO @ Thu, 09 Dec 2021 03:15:08: 12000000 INFO @ Thu, 09 Dec 2021 03:15:09: 24000000 INFO @ Thu, 09 Dec 2021 03:15:10: 18000000 INFO @ Thu, 09 Dec 2021 03:15:13: 13000000 INFO @ Thu, 09 Dec 2021 03:15:15: 25000000 INFO @ Thu, 09 Dec 2021 03:15:15: 19000000 INFO @ Thu, 09 Dec 2021 03:15:18: 14000000 INFO @ Thu, 09 Dec 2021 03:15:20: 26000000 INFO @ Thu, 09 Dec 2021 03:15:21: 20000000 INFO @ Thu, 09 Dec 2021 03:15:24: 15000000 INFO @ Thu, 09 Dec 2021 03:15:25: 27000000 INFO @ Thu, 09 Dec 2021 03:15:26: 21000000 INFO @ Thu, 09 Dec 2021 03:15:29: 16000000 INFO @ Thu, 09 Dec 2021 03:15:31: 28000000 INFO @ Thu, 09 Dec 2021 03:15:31: 22000000 INFO @ Thu, 09 Dec 2021 03:15:34: 17000000 INFO @ Thu, 09 Dec 2021 03:15:36: 29000000 INFO @ Thu, 09 Dec 2021 03:15:37: 23000000 INFO @ Thu, 09 Dec 2021 03:15:40: 18000000 INFO @ Thu, 09 Dec 2021 03:15:41: 30000000 INFO @ Thu, 09 Dec 2021 03:15:42: 24000000 INFO @ Thu, 09 Dec 2021 03:15:45: 19000000 INFO @ Thu, 09 Dec 2021 03:15:47: 31000000 INFO @ Thu, 09 Dec 2021 03:15:47: 25000000 INFO @ Thu, 09 Dec 2021 03:15:50: 20000000 INFO @ Thu, 09 Dec 2021 03:15:52: 32000000 INFO @ Thu, 09 Dec 2021 03:15:52: 26000000 INFO @ Thu, 09 Dec 2021 03:15:55: 21000000 INFO @ Thu, 09 Dec 2021 03:15:57: 33000000 INFO @ Thu, 09 Dec 2021 03:15:58: 27000000 INFO @ Thu, 09 Dec 2021 03:16:01: 22000000 INFO @ Thu, 09 Dec 2021 03:16:02: 34000000 INFO @ Thu, 09 Dec 2021 03:16:03: 28000000 INFO @ Thu, 09 Dec 2021 03:16:06: 23000000 INFO @ Thu, 09 Dec 2021 03:16:08: 35000000 INFO @ Thu, 09 Dec 2021 03:16:08: 29000000 INFO @ Thu, 09 Dec 2021 03:16:12: 24000000 INFO @ Thu, 09 Dec 2021 03:16:13: 36000000 INFO @ Thu, 09 Dec 2021 03:16:13: 30000000 INFO @ Thu, 09 Dec 2021 03:16:17: 25000000 INFO @ Thu, 09 Dec 2021 03:16:18: 37000000 INFO @ Thu, 09 Dec 2021 03:16:19: 31000000 INFO @ Thu, 09 Dec 2021 03:16:22: 26000000 INFO @ Thu, 09 Dec 2021 03:16:24: 38000000 INFO @ Thu, 09 Dec 2021 03:16:24: 32000000 INFO @ Thu, 09 Dec 2021 03:16:27: 27000000 INFO @ Thu, 09 Dec 2021 03:16:29: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:16:29: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:16:29: #1 total tags in treatment: 18581027 INFO @ Thu, 09 Dec 2021 03:16:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:16:29: #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 03:16:29: #1 tags after filtering in treatment: 16842205 INFO @ Thu, 09 Dec 2021 03:16:29: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:16:29: #1 finished! INFO @ Thu, 09 Dec 2021 03:16:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:16:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:16:29: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:16:30: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:16:30: 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 03:16:30: start model_add_line... INFO @ Thu, 09 Dec 2021 03:16:30: start X-correlation... INFO @ Thu, 09 Dec 2021 03:16:30: end of X-cor INFO @ Thu, 09 Dec 2021 03:16:30: #2 finished! INFO @ Thu, 09 Dec 2021 03:16:30: #2 predicted fragment length is 123 bps INFO @ Thu, 09 Dec 2021 03:16:30: #2 alternative fragment length(s) may be 3,123 bps INFO @ Thu, 09 Dec 2021 03:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.05_model.r INFO @ Thu, 09 Dec 2021 03:16:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:16:33: 28000000 INFO @ Thu, 09 Dec 2021 03:16:34: 34000000 INFO @ Thu, 09 Dec 2021 03:16:38: 29000000 INFO @ Thu, 09 Dec 2021 03:16:40: 35000000 INFO @ Thu, 09 Dec 2021 03:16:43: 30000000 INFO @ Thu, 09 Dec 2021 03:16:45: 36000000 INFO @ Thu, 09 Dec 2021 03:16:48: 31000000 INFO @ Thu, 09 Dec 2021 03:16:50: 37000000 INFO @ Thu, 09 Dec 2021 03:16:53: 32000000 INFO @ Thu, 09 Dec 2021 03:16:55: 38000000 INFO @ Thu, 09 Dec 2021 03:16:59: 33000000 INFO @ Thu, 09 Dec 2021 03:17:00: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:17:00: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:17:00: #1 total tags in treatment: 18581027 INFO @ Thu, 09 Dec 2021 03:17:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:17:00: #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 03:17:00: #1 tags after filtering in treatment: 16842205 INFO @ Thu, 09 Dec 2021 03:17:00: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:17:00: #1 finished! INFO @ Thu, 09 Dec 2021 03:17:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:17:00: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:17:01: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:17:01: 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 03:17:01: start model_add_line... INFO @ Thu, 09 Dec 2021 03:17:02: start X-correlation... INFO @ Thu, 09 Dec 2021 03:17:02: end of X-cor INFO @ Thu, 09 Dec 2021 03:17:02: #2 finished! INFO @ Thu, 09 Dec 2021 03:17:02: #2 predicted fragment length is 123 bps INFO @ Thu, 09 Dec 2021 03:17:02: #2 alternative fragment length(s) may be 3,123 bps INFO @ Thu, 09 Dec 2021 03:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.10_model.r INFO @ Thu, 09 Dec 2021 03:17:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:17:03: 34000000 INFO @ Thu, 09 Dec 2021 03:17:08: 35000000 INFO @ Thu, 09 Dec 2021 03:17:13: 36000000 INFO @ Thu, 09 Dec 2021 03:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.05_summits.bed INFO @ Thu, 09 Dec 2021 03:17:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1870 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:17:18: 37000000 INFO @ Thu, 09 Dec 2021 03:17:23: 38000000 INFO @ Thu, 09 Dec 2021 03:17:27: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:17:27: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:17:27: #1 total tags in treatment: 18581027 INFO @ Thu, 09 Dec 2021 03:17:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:17:27: #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 03:17:27: #1 tags after filtering in treatment: 16842205 INFO @ Thu, 09 Dec 2021 03:17:27: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:17:27: #1 finished! INFO @ Thu, 09 Dec 2021 03:17:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:17:28: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 03:17:28: 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 03:17:28: start model_add_line... INFO @ Thu, 09 Dec 2021 03:17:28: start X-correlation... INFO @ Thu, 09 Dec 2021 03:17:28: end of X-cor INFO @ Thu, 09 Dec 2021 03:17:28: #2 finished! INFO @ Thu, 09 Dec 2021 03:17:28: #2 predicted fragment length is 123 bps INFO @ Thu, 09 Dec 2021 03:17:28: #2 alternative fragment length(s) may be 3,123 bps INFO @ Thu, 09 Dec 2021 03:17:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.20_model.r INFO @ Thu, 09 Dec 2021 03:17:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:17:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:17:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:17:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:17:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:17:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.10_summits.bed INFO @ Thu, 09 Dec 2021 03:17:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (949 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:17:59: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555459/SRX9555459.20_summits.bed INFO @ Thu, 09 Dec 2021 03:18:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 1 millis CompletedMACS2peakCalling