Job ID = 14158317 SRX = SRX10342591 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9550913 spots for SRR13964638/SRR13964638.sra Written 9550913 spots for SRR13964638/SRR13964638.sra Read 10420965 spots for SRR13964639/SRR13964639.sra Written 10420965 spots for SRR13964639/SRR13964639.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158857 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:03 19971878 reads; of these: 19971878 (100.00%) were paired; of these: 8985089 (44.99%) aligned concordantly 0 times 9552813 (47.83%) aligned concordantly exactly 1 time 1433976 (7.18%) aligned concordantly >1 times ---- 8985089 pairs aligned concordantly 0 times; of these: 5107803 (56.85%) aligned discordantly 1 time ---- 3877286 pairs aligned 0 times concordantly or discordantly; of these: 7754572 mates make up the pairs; of these: 5902358 (76.11%) aligned 0 times 760320 (9.80%) aligned exactly 1 time 1091894 (14.08%) aligned >1 times 85.22% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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] 6780405 / 16088581 = 0.4214 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 16:18:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.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 16:18:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:18:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:18:29: 1000000 INFO @ Wed, 08 Dec 2021 16:18:34: 2000000 INFO @ Wed, 08 Dec 2021 16:18:38: 3000000 INFO @ Wed, 08 Dec 2021 16:18:42: 4000000 INFO @ Wed, 08 Dec 2021 16:18:47: 5000000 INFO @ Wed, 08 Dec 2021 16:18:51: 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 @ Wed, 08 Dec 2021 16:18:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.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 16:18:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:18:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:18:55: 7000000 INFO @ Wed, 08 Dec 2021 16:18:59: 1000000 INFO @ Wed, 08 Dec 2021 16:19:00: 8000000 INFO @ Wed, 08 Dec 2021 16:19:03: 2000000 INFO @ Wed, 08 Dec 2021 16:19:04: 9000000 INFO @ Wed, 08 Dec 2021 16:19:07: 3000000 INFO @ Wed, 08 Dec 2021 16:19:09: 10000000 INFO @ Wed, 08 Dec 2021 16:19:11: 4000000 INFO @ Wed, 08 Dec 2021 16:19:13: 11000000 INFO @ Wed, 08 Dec 2021 16:19:14: 5000000 INFO @ Wed, 08 Dec 2021 16:19:18: 12000000 INFO @ Wed, 08 Dec 2021 16:19:18: 6000000 INFO @ Wed, 08 Dec 2021 16:19:22: 13000000 INFO @ Wed, 08 Dec 2021 16:19:22: 7000000 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 16:19:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.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 16:19:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:19:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:19:26: 8000000 INFO @ Wed, 08 Dec 2021 16:19:26: 14000000 INFO @ Wed, 08 Dec 2021 16:19:29: 1000000 INFO @ Wed, 08 Dec 2021 16:19:30: 9000000 INFO @ Wed, 08 Dec 2021 16:19:31: 15000000 INFO @ Wed, 08 Dec 2021 16:19:34: 2000000 INFO @ Wed, 08 Dec 2021 16:19:34: 10000000 INFO @ Wed, 08 Dec 2021 16:19:35: 16000000 INFO @ Wed, 08 Dec 2021 16:19:38: 11000000 INFO @ Wed, 08 Dec 2021 16:19:38: 3000000 INFO @ Wed, 08 Dec 2021 16:19:40: 17000000 INFO @ Wed, 08 Dec 2021 16:19:42: 12000000 INFO @ Wed, 08 Dec 2021 16:19:43: 4000000 INFO @ Wed, 08 Dec 2021 16:19:44: 18000000 INFO @ Wed, 08 Dec 2021 16:19:46: 13000000 INFO @ Wed, 08 Dec 2021 16:19:47: 5000000 INFO @ Wed, 08 Dec 2021 16:19:48: 19000000 INFO @ Wed, 08 Dec 2021 16:19:49: 14000000 INFO @ Wed, 08 Dec 2021 16:19:51: 6000000 INFO @ Wed, 08 Dec 2021 16:19:53: 20000000 INFO @ Wed, 08 Dec 2021 16:19:53: 15000000 INFO @ Wed, 08 Dec 2021 16:19:55: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:19:55: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:19:55: #1 total tags in treatment: 5988560 INFO @ Wed, 08 Dec 2021 16:19:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:19:55: #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 16:19:55: #1 tags after filtering in treatment: 5620159 INFO @ Wed, 08 Dec 2021 16:19:55: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 16:19:55: #1 finished! INFO @ Wed, 08 Dec 2021 16:19:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:19:55: #2 number of paired peaks: 677 WARNING @ Wed, 08 Dec 2021 16:19:55: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Wed, 08 Dec 2021 16:19:55: start model_add_line... INFO @ Wed, 08 Dec 2021 16:19:55: start X-correlation... INFO @ Wed, 08 Dec 2021 16:19:55: end of X-cor INFO @ Wed, 08 Dec 2021 16:19:55: #2 finished! INFO @ Wed, 08 Dec 2021 16:19:55: #2 predicted fragment length is 158 bps INFO @ Wed, 08 Dec 2021 16:19:55: #2 alternative fragment length(s) may be 4,158 bps INFO @ Wed, 08 Dec 2021 16:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.05_model.r INFO @ Wed, 08 Dec 2021 16:19:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:19:56: 7000000 INFO @ Wed, 08 Dec 2021 16:19:57: 16000000 INFO @ Wed, 08 Dec 2021 16:20:00: 8000000 INFO @ Wed, 08 Dec 2021 16:20:01: 17000000 INFO @ Wed, 08 Dec 2021 16:20:05: 9000000 INFO @ Wed, 08 Dec 2021 16:20:05: 18000000 INFO @ Wed, 08 Dec 2021 16:20:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:20:09: 19000000 INFO @ Wed, 08 Dec 2021 16:20:09: 10000000 INFO @ Wed, 08 Dec 2021 16:20:13: 20000000 INFO @ Wed, 08 Dec 2021 16:20:14: 11000000 INFO @ Wed, 08 Dec 2021 16:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.05_summits.bed INFO @ Wed, 08 Dec 2021 16:20:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1459 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:20:14: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:20:14: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:20:14: #1 total tags in treatment: 5988560 INFO @ Wed, 08 Dec 2021 16:20:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:20:14: #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 16:20:15: #1 tags after filtering in treatment: 5620159 INFO @ Wed, 08 Dec 2021 16:20:15: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 16:20:15: #1 finished! INFO @ Wed, 08 Dec 2021 16:20:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:20:15: #2 number of paired peaks: 677 WARNING @ Wed, 08 Dec 2021 16:20:15: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Wed, 08 Dec 2021 16:20:15: start model_add_line... INFO @ Wed, 08 Dec 2021 16:20:15: start X-correlation... INFO @ Wed, 08 Dec 2021 16:20:15: end of X-cor INFO @ Wed, 08 Dec 2021 16:20:15: #2 finished! INFO @ Wed, 08 Dec 2021 16:20:15: #2 predicted fragment length is 158 bps INFO @ Wed, 08 Dec 2021 16:20:15: #2 alternative fragment length(s) may be 4,158 bps INFO @ Wed, 08 Dec 2021 16:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.10_model.r INFO @ Wed, 08 Dec 2021 16:20:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:20:18: 12000000 INFO @ Wed, 08 Dec 2021 16:20:22: 13000000 INFO @ Wed, 08 Dec 2021 16:20:26: 14000000 INFO @ Wed, 08 Dec 2021 16:20:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:20:31: 15000000 INFO @ Wed, 08 Dec 2021 16:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.10_summits.bed INFO @ Wed, 08 Dec 2021 16:20:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (450 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:20:35: 16000000 INFO @ Wed, 08 Dec 2021 16:20:39: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:20:43: 18000000 INFO @ Wed, 08 Dec 2021 16:20:48: 19000000 INFO @ Wed, 08 Dec 2021 16:20:52: 20000000 INFO @ Wed, 08 Dec 2021 16:20:54: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:20:54: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:20:54: #1 total tags in treatment: 5988560 INFO @ Wed, 08 Dec 2021 16:20:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:20:54: #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 16:20:54: #1 tags after filtering in treatment: 5620159 INFO @ Wed, 08 Dec 2021 16:20:54: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 16:20:54: #1 finished! INFO @ Wed, 08 Dec 2021 16:20:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:20:55: #2 number of paired peaks: 677 WARNING @ Wed, 08 Dec 2021 16:20:55: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Wed, 08 Dec 2021 16:20:55: start model_add_line... INFO @ Wed, 08 Dec 2021 16:20:55: start X-correlation... INFO @ Wed, 08 Dec 2021 16:20:55: end of X-cor INFO @ Wed, 08 Dec 2021 16:20:55: #2 finished! INFO @ Wed, 08 Dec 2021 16:20:55: #2 predicted fragment length is 158 bps INFO @ Wed, 08 Dec 2021 16:20:55: #2 alternative fragment length(s) may be 4,158 bps INFO @ Wed, 08 Dec 2021 16:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.20_model.r INFO @ Wed, 08 Dec 2021 16:20:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:21:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342591/SRX10342591.20_summits.bed INFO @ Wed, 08 Dec 2021 16:21:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。