Job ID = 14158916 SRX = SRX8976716 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14145439 spots for SRR12483320/SRR12483320.sra Written 14145439 spots for SRR12483320/SRR12483320.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159272 ("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: 00:12:02 14145439 reads; of these: 14145439 (100.00%) were paired; of these: 233183 (1.65%) aligned concordantly 0 times 12064871 (85.29%) aligned concordantly exactly 1 time 1847385 (13.06%) aligned concordantly >1 times ---- 233183 pairs aligned concordantly 0 times; of these: 90219 (38.69%) aligned discordantly 1 time ---- 142964 pairs aligned 0 times concordantly or discordantly; of these: 285928 mates make up the pairs; of these: 174161 (60.91%) aligned 0 times 70312 (24.59%) aligned exactly 1 time 41455 (14.50%) aligned >1 times 99.38% overall alignment rate Time searching: 00:12:02 Overall time: 00:12:02 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] 179413 / 13987392 = 0.0128 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 18:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.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 18:40:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:40:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:40:46: 1000000 INFO @ Wed, 08 Dec 2021 18:40:51: 2000000 INFO @ Wed, 08 Dec 2021 18:40:55: 3000000 INFO @ Wed, 08 Dec 2021 18:40:59: 4000000 INFO @ Wed, 08 Dec 2021 18:41:03: 5000000 INFO @ Wed, 08 Dec 2021 18:41:08: 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 18:41:12: 7000000 INFO @ Wed, 08 Dec 2021 18:41:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.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 18:41:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:41:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:41:16: 8000000 INFO @ Wed, 08 Dec 2021 18:41:17: 1000000 INFO @ Wed, 08 Dec 2021 18:41:21: 9000000 INFO @ Wed, 08 Dec 2021 18:41:22: 2000000 INFO @ Wed, 08 Dec 2021 18:41:26: 10000000 INFO @ Wed, 08 Dec 2021 18:41:27: 3000000 INFO @ Wed, 08 Dec 2021 18:41:30: 11000000 INFO @ Wed, 08 Dec 2021 18:41:32: 4000000 INFO @ Wed, 08 Dec 2021 18:41:35: 12000000 INFO @ Wed, 08 Dec 2021 18:41:38: 5000000 INFO @ Wed, 08 Dec 2021 18:41:39: 13000000 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 18:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.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 18:41:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:41:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:41:43: 6000000 INFO @ Wed, 08 Dec 2021 18:41:44: 14000000 INFO @ Wed, 08 Dec 2021 18:41:47: 1000000 INFO @ Wed, 08 Dec 2021 18:41:48: 7000000 INFO @ Wed, 08 Dec 2021 18:41:49: 15000000 INFO @ Wed, 08 Dec 2021 18:41:51: 2000000 INFO @ Wed, 08 Dec 2021 18:41:53: 16000000 INFO @ Wed, 08 Dec 2021 18:41:53: 8000000 INFO @ Wed, 08 Dec 2021 18:41:56: 3000000 INFO @ Wed, 08 Dec 2021 18:41:58: 17000000 INFO @ Wed, 08 Dec 2021 18:41:59: 9000000 INFO @ Wed, 08 Dec 2021 18:42:02: 4000000 INFO @ Wed, 08 Dec 2021 18:42:03: 18000000 INFO @ Wed, 08 Dec 2021 18:42:04: 10000000 INFO @ Wed, 08 Dec 2021 18:42:07: 5000000 INFO @ Wed, 08 Dec 2021 18:42:08: 19000000 INFO @ Wed, 08 Dec 2021 18:42:10: 11000000 INFO @ Wed, 08 Dec 2021 18:42:13: 6000000 INFO @ Wed, 08 Dec 2021 18:42:13: 20000000 INFO @ Wed, 08 Dec 2021 18:42:16: 12000000 INFO @ Wed, 08 Dec 2021 18:42:18: 21000000 INFO @ Wed, 08 Dec 2021 18:42:19: 7000000 INFO @ Wed, 08 Dec 2021 18:42:22: 13000000 INFO @ Wed, 08 Dec 2021 18:42:24: 22000000 INFO @ Wed, 08 Dec 2021 18:42:26: 8000000 INFO @ Wed, 08 Dec 2021 18:42:28: 14000000 INFO @ Wed, 08 Dec 2021 18:42:28: 23000000 INFO @ Wed, 08 Dec 2021 18:42:33: 9000000 INFO @ Wed, 08 Dec 2021 18:42:33: 15000000 INFO @ Wed, 08 Dec 2021 18:42:34: 24000000 INFO @ Wed, 08 Dec 2021 18:42:39: 25000000 INFO @ Wed, 08 Dec 2021 18:42:39: 16000000 INFO @ Wed, 08 Dec 2021 18:42:39: 10000000 INFO @ Wed, 08 Dec 2021 18:42:44: 26000000 INFO @ Wed, 08 Dec 2021 18:42:44: 11000000 INFO @ Wed, 08 Dec 2021 18:42:45: 17000000 INFO @ Wed, 08 Dec 2021 18:42:49: 27000000 INFO @ Wed, 08 Dec 2021 18:42:49: 12000000 INFO @ Wed, 08 Dec 2021 18:42:50: 18000000 INFO @ Wed, 08 Dec 2021 18:42:53: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:42:53: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:42:53: #1 total tags in treatment: 13733466 INFO @ Wed, 08 Dec 2021 18:42:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:42:53: #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 18:42:53: #1 tags after filtering in treatment: 12837587 INFO @ Wed, 08 Dec 2021 18:42:53: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:42:53: #1 finished! INFO @ Wed, 08 Dec 2021 18:42:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:42:54: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:42:54: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:42:54: start model_add_line... INFO @ Wed, 08 Dec 2021 18:42:54: 13000000 INFO @ Wed, 08 Dec 2021 18:42:54: start X-correlation... INFO @ Wed, 08 Dec 2021 18:42:54: end of X-cor INFO @ Wed, 08 Dec 2021 18:42:54: #2 finished! INFO @ Wed, 08 Dec 2021 18:42:54: #2 predicted fragment length is 152 bps INFO @ Wed, 08 Dec 2021 18:42:54: #2 alternative fragment length(s) may be 4,152 bps INFO @ Wed, 08 Dec 2021 18:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.05_model.r INFO @ Wed, 08 Dec 2021 18:42:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:42:56: 19000000 INFO @ Wed, 08 Dec 2021 18:42:59: 14000000 INFO @ Wed, 08 Dec 2021 18:43:02: 20000000 INFO @ Wed, 08 Dec 2021 18:43:04: 15000000 INFO @ Wed, 08 Dec 2021 18:43:09: 21000000 INFO @ Wed, 08 Dec 2021 18:43:09: 16000000 INFO @ Wed, 08 Dec 2021 18:43:14: 17000000 INFO @ Wed, 08 Dec 2021 18:43:15: 22000000 INFO @ Wed, 08 Dec 2021 18:43:18: 18000000 INFO @ Wed, 08 Dec 2021 18:43:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:43:20: 23000000 INFO @ Wed, 08 Dec 2021 18:43:23: 19000000 INFO @ Wed, 08 Dec 2021 18:43:26: 24000000 INFO @ Wed, 08 Dec 2021 18:43:28: 20000000 INFO @ Wed, 08 Dec 2021 18:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.05_summits.bed INFO @ Wed, 08 Dec 2021 18:43:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:43:32: 25000000 INFO @ Wed, 08 Dec 2021 18:43:33: 21000000 INFO @ Wed, 08 Dec 2021 18:43:37: 26000000 INFO @ Wed, 08 Dec 2021 18:43:38: 22000000 INFO @ Wed, 08 Dec 2021 18:43:43: 27000000 INFO @ Wed, 08 Dec 2021 18:43:43: 23000000 INFO @ Wed, 08 Dec 2021 18:43:47: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:43:47: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:43:47: #1 total tags in treatment: 13733466 INFO @ Wed, 08 Dec 2021 18:43:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:43:47: #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 18:43:47: #1 tags after filtering in treatment: 12837587 INFO @ Wed, 08 Dec 2021 18:43:47: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:43:47: #1 finished! INFO @ Wed, 08 Dec 2021 18:43:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:43:48: 24000000 INFO @ Wed, 08 Dec 2021 18:43:48: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:43:48: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:43:48: start model_add_line... INFO @ Wed, 08 Dec 2021 18:43:49: start X-correlation... INFO @ Wed, 08 Dec 2021 18:43:49: end of X-cor INFO @ Wed, 08 Dec 2021 18:43:49: #2 finished! INFO @ Wed, 08 Dec 2021 18:43:49: #2 predicted fragment length is 152 bps INFO @ Wed, 08 Dec 2021 18:43:49: #2 alternative fragment length(s) may be 4,152 bps INFO @ Wed, 08 Dec 2021 18:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.10_model.r INFO @ Wed, 08 Dec 2021 18:43:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:43:52: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:43:57: 26000000 INFO @ Wed, 08 Dec 2021 18:44:01: 27000000 INFO @ Wed, 08 Dec 2021 18:44:05: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:44:05: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:44:05: #1 total tags in treatment: 13733466 INFO @ Wed, 08 Dec 2021 18:44:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:44:05: #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 18:44:05: #1 tags after filtering in treatment: 12837587 INFO @ Wed, 08 Dec 2021 18:44:05: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:44:05: #1 finished! INFO @ Wed, 08 Dec 2021 18:44:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:44:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:44:06: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:44:06: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:44:06: start model_add_line... INFO @ Wed, 08 Dec 2021 18:44:06: start X-correlation... INFO @ Wed, 08 Dec 2021 18:44:06: end of X-cor INFO @ Wed, 08 Dec 2021 18:44:06: #2 finished! INFO @ Wed, 08 Dec 2021 18:44:06: #2 predicted fragment length is 152 bps INFO @ Wed, 08 Dec 2021 18:44:06: #2 alternative fragment length(s) may be 4,152 bps INFO @ Wed, 08 Dec 2021 18:44:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.20_model.r INFO @ Wed, 08 Dec 2021 18:44:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:44:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:44:12: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.10_summits.bed INFO @ Wed, 08 Dec 2021 18:44:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (267 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:44:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:44:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:44:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976716/SRX8976716.20_summits.bed INFO @ Wed, 08 Dec 2021 18:44:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。