Job ID = 14158337 SRX = SRX10342598 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10778723 spots for SRR13964652/SRR13964652.sra Written 10778723 spots for SRR13964652/SRR13964652.sra Read 11932776 spots for SRR13964653/SRR13964653.sra Written 11932776 spots for SRR13964653/SRR13964653.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158927 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:45 22711499 reads; of these: 22711499 (100.00%) were paired; of these: 5357807 (23.59%) aligned concordantly 0 times 15101258 (66.49%) aligned concordantly exactly 1 time 2252434 (9.92%) aligned concordantly >1 times ---- 5357807 pairs aligned concordantly 0 times; of these: 3544410 (66.15%) aligned discordantly 1 time ---- 1813397 pairs aligned 0 times concordantly or discordantly; of these: 3626794 mates make up the pairs; of these: 2208497 (60.89%) aligned 0 times 581532 (16.03%) aligned exactly 1 time 836765 (23.07%) aligned >1 times 95.14% overall alignment rate Time searching: 00:15:46 Overall time: 00:15:46 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] 2768884 / 20889568 = 0.1325 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 16:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.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 16:41:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:41:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:41:31: 1000000 INFO @ Wed, 08 Dec 2021 16:41:36: 2000000 INFO @ Wed, 08 Dec 2021 16:41:40: 3000000 INFO @ Wed, 08 Dec 2021 16:41:45: 4000000 INFO @ Wed, 08 Dec 2021 16:41:49: 5000000 INFO @ Wed, 08 Dec 2021 16:41:54: 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 16:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.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 16:41:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:41:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:41:59: 7000000 INFO @ Wed, 08 Dec 2021 16:42:02: 1000000 INFO @ Wed, 08 Dec 2021 16:42:04: 8000000 INFO @ Wed, 08 Dec 2021 16:42:07: 2000000 INFO @ Wed, 08 Dec 2021 16:42:09: 9000000 INFO @ Wed, 08 Dec 2021 16:42:12: 3000000 INFO @ Wed, 08 Dec 2021 16:42:15: 10000000 INFO @ Wed, 08 Dec 2021 16:42:17: 4000000 INFO @ Wed, 08 Dec 2021 16:42:20: 11000000 INFO @ Wed, 08 Dec 2021 16:42:23: 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 @ Wed, 08 Dec 2021 16:42:25: 12000000 INFO @ Wed, 08 Dec 2021 16:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.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 16:42:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:42:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:42:28: 6000000 INFO @ Wed, 08 Dec 2021 16:42:30: 13000000 INFO @ Wed, 08 Dec 2021 16:42:32: 1000000 INFO @ Wed, 08 Dec 2021 16:42:33: 7000000 INFO @ Wed, 08 Dec 2021 16:42:36: 14000000 INFO @ Wed, 08 Dec 2021 16:42:37: 2000000 INFO @ Wed, 08 Dec 2021 16:42:38: 8000000 INFO @ Wed, 08 Dec 2021 16:42:41: 15000000 INFO @ Wed, 08 Dec 2021 16:42:42: 3000000 INFO @ Wed, 08 Dec 2021 16:42:44: 9000000 INFO @ Wed, 08 Dec 2021 16:42:46: 16000000 INFO @ Wed, 08 Dec 2021 16:42:47: 4000000 INFO @ Wed, 08 Dec 2021 16:42:49: 10000000 INFO @ Wed, 08 Dec 2021 16:42:52: 17000000 INFO @ Wed, 08 Dec 2021 16:42:53: 5000000 INFO @ Wed, 08 Dec 2021 16:42:54: 11000000 INFO @ Wed, 08 Dec 2021 16:42:57: 18000000 INFO @ Wed, 08 Dec 2021 16:42:58: 6000000 INFO @ Wed, 08 Dec 2021 16:42:59: 12000000 INFO @ Wed, 08 Dec 2021 16:43:02: 19000000 INFO @ Wed, 08 Dec 2021 16:43:03: 7000000 INFO @ Wed, 08 Dec 2021 16:43:05: 13000000 INFO @ Wed, 08 Dec 2021 16:43:07: 20000000 INFO @ Wed, 08 Dec 2021 16:43:09: 8000000 INFO @ Wed, 08 Dec 2021 16:43:10: 14000000 INFO @ Wed, 08 Dec 2021 16:43:13: 21000000 INFO @ Wed, 08 Dec 2021 16:43:14: 9000000 INFO @ Wed, 08 Dec 2021 16:43:15: 15000000 INFO @ Wed, 08 Dec 2021 16:43:18: 22000000 INFO @ Wed, 08 Dec 2021 16:43:19: 10000000 INFO @ Wed, 08 Dec 2021 16:43:21: 16000000 INFO @ Wed, 08 Dec 2021 16:43:23: 23000000 INFO @ Wed, 08 Dec 2021 16:43:24: 11000000 INFO @ Wed, 08 Dec 2021 16:43:26: 17000000 INFO @ Wed, 08 Dec 2021 16:43:29: 24000000 INFO @ Wed, 08 Dec 2021 16:43:30: 12000000 INFO @ Wed, 08 Dec 2021 16:43:31: 18000000 INFO @ Wed, 08 Dec 2021 16:43:34: 25000000 INFO @ Wed, 08 Dec 2021 16:43:35: 13000000 INFO @ Wed, 08 Dec 2021 16:43:36: 19000000 INFO @ Wed, 08 Dec 2021 16:43:39: 26000000 INFO @ Wed, 08 Dec 2021 16:43:40: 14000000 INFO @ Wed, 08 Dec 2021 16:43:42: 20000000 INFO @ Wed, 08 Dec 2021 16:43:44: 27000000 INFO @ Wed, 08 Dec 2021 16:43:45: 15000000 INFO @ Wed, 08 Dec 2021 16:43:47: 21000000 INFO @ Wed, 08 Dec 2021 16:43:50: 28000000 INFO @ Wed, 08 Dec 2021 16:43:51: 16000000 INFO @ Wed, 08 Dec 2021 16:43:52: 22000000 INFO @ Wed, 08 Dec 2021 16:43:55: 29000000 INFO @ Wed, 08 Dec 2021 16:43:56: 17000000 INFO @ Wed, 08 Dec 2021 16:43:58: 23000000 INFO @ Wed, 08 Dec 2021 16:44:00: 30000000 INFO @ Wed, 08 Dec 2021 16:44:01: 18000000 INFO @ Wed, 08 Dec 2021 16:44:03: 24000000 INFO @ Wed, 08 Dec 2021 16:44:06: 31000000 INFO @ Wed, 08 Dec 2021 16:44:07: 19000000 INFO @ Wed, 08 Dec 2021 16:44:08: 25000000 INFO @ Wed, 08 Dec 2021 16:44:11: 32000000 INFO @ Wed, 08 Dec 2021 16:44:12: 20000000 INFO @ Wed, 08 Dec 2021 16:44:13: 26000000 INFO @ Wed, 08 Dec 2021 16:44:16: 33000000 INFO @ Wed, 08 Dec 2021 16:44:17: 21000000 INFO @ Wed, 08 Dec 2021 16:44:19: 27000000 INFO @ Wed, 08 Dec 2021 16:44:21: 34000000 INFO @ Wed, 08 Dec 2021 16:44:22: 22000000 INFO @ Wed, 08 Dec 2021 16:44:24: 28000000 INFO @ Wed, 08 Dec 2021 16:44:27: 35000000 INFO @ Wed, 08 Dec 2021 16:44:28: 23000000 INFO @ Wed, 08 Dec 2021 16:44:29: 29000000 INFO @ Wed, 08 Dec 2021 16:44:32: 36000000 INFO @ Wed, 08 Dec 2021 16:44:33: 24000000 INFO @ Wed, 08 Dec 2021 16:44:34: 30000000 INFO @ Wed, 08 Dec 2021 16:44:37: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:44:38: 25000000 INFO @ Wed, 08 Dec 2021 16:44:40: 31000000 INFO @ Wed, 08 Dec 2021 16:44:41: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:44:41: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:44:41: #1 total tags in treatment: 14967050 INFO @ Wed, 08 Dec 2021 16:44:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:44:41: #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 16:44:41: #1 tags after filtering in treatment: 13620055 INFO @ Wed, 08 Dec 2021 16:44:41: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:44:41: #1 finished! INFO @ Wed, 08 Dec 2021 16:44:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:44:42: #2 number of paired peaks: 347 WARNING @ Wed, 08 Dec 2021 16:44:42: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Wed, 08 Dec 2021 16:44:42: start model_add_line... INFO @ Wed, 08 Dec 2021 16:44:42: start X-correlation... INFO @ Wed, 08 Dec 2021 16:44:42: end of X-cor INFO @ Wed, 08 Dec 2021 16:44:42: #2 finished! INFO @ Wed, 08 Dec 2021 16:44:42: #2 predicted fragment length is 139 bps INFO @ Wed, 08 Dec 2021 16:44:42: #2 alternative fragment length(s) may be 3,139 bps INFO @ Wed, 08 Dec 2021 16:44:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.05_model.r INFO @ Wed, 08 Dec 2021 16:44:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:44:44: 26000000 INFO @ Wed, 08 Dec 2021 16:44:45: 32000000 INFO @ Wed, 08 Dec 2021 16:44:49: 27000000 INFO @ Wed, 08 Dec 2021 16:44:50: 33000000 INFO @ Wed, 08 Dec 2021 16:44:54: 28000000 INFO @ Wed, 08 Dec 2021 16:44:56: 34000000 INFO @ Wed, 08 Dec 2021 16:44:59: 29000000 INFO @ Wed, 08 Dec 2021 16:45:01: 35000000 INFO @ Wed, 08 Dec 2021 16:45:05: 30000000 INFO @ Wed, 08 Dec 2021 16:45:06: 36000000 INFO @ Wed, 08 Dec 2021 16:45:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:45:10: 31000000 INFO @ Wed, 08 Dec 2021 16:45:11: 37000000 INFO @ Wed, 08 Dec 2021 16:45:15: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:45:15: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:45:15: #1 total tags in treatment: 14967050 INFO @ Wed, 08 Dec 2021 16:45:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:45:15: #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 16:45:15: #1 tags after filtering in treatment: 13620055 INFO @ Wed, 08 Dec 2021 16:45:15: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:45:15: #1 finished! INFO @ Wed, 08 Dec 2021 16:45:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:45:15: 32000000 INFO @ Wed, 08 Dec 2021 16:45:16: #2 number of paired peaks: 347 WARNING @ Wed, 08 Dec 2021 16:45:16: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Wed, 08 Dec 2021 16:45:16: start model_add_line... INFO @ Wed, 08 Dec 2021 16:45:16: start X-correlation... INFO @ Wed, 08 Dec 2021 16:45:16: end of X-cor INFO @ Wed, 08 Dec 2021 16:45:16: #2 finished! INFO @ Wed, 08 Dec 2021 16:45:16: #2 predicted fragment length is 139 bps INFO @ Wed, 08 Dec 2021 16:45:16: #2 alternative fragment length(s) may be 3,139 bps INFO @ Wed, 08 Dec 2021 16:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.10_model.r INFO @ Wed, 08 Dec 2021 16:45:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:45:20: 33000000 INFO @ Wed, 08 Dec 2021 16:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.05_summits.bed INFO @ Wed, 08 Dec 2021 16:45:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1760 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:45:25: 34000000 INFO @ Wed, 08 Dec 2021 16:45:30: 35000000 INFO @ Wed, 08 Dec 2021 16:45:34: 36000000 INFO @ Wed, 08 Dec 2021 16:45:39: 37000000 INFO @ Wed, 08 Dec 2021 16:45:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:45:42: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:45:42: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:45:42: #1 total tags in treatment: 14967050 INFO @ Wed, 08 Dec 2021 16:45:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:45:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:45:42: #1 tags after filtering in treatment: 13620055 INFO @ Wed, 08 Dec 2021 16:45:42: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:45:42: #1 finished! INFO @ Wed, 08 Dec 2021 16:45:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:45:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:45:43: #2 number of paired peaks: 347 WARNING @ Wed, 08 Dec 2021 16:45:43: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Wed, 08 Dec 2021 16:45:43: start model_add_line... INFO @ Wed, 08 Dec 2021 16:45:43: start X-correlation... INFO @ Wed, 08 Dec 2021 16:45:43: end of X-cor INFO @ Wed, 08 Dec 2021 16:45:43: #2 finished! INFO @ Wed, 08 Dec 2021 16:45:43: #2 predicted fragment length is 139 bps INFO @ Wed, 08 Dec 2021 16:45:43: #2 alternative fragment length(s) may be 3,139 bps INFO @ Wed, 08 Dec 2021 16:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.20_model.r INFO @ Wed, 08 Dec 2021 16:45:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.10_summits.bed INFO @ Wed, 08 Dec 2021 16:45:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (508 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:46:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342598/SRX10342598.20_summits.bed INFO @ Wed, 08 Dec 2021 16:46:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling