Job ID = 14158495 SRX = SRX8976700 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13717587 spots for SRR12483304/SRR12483304.sra Written 13717587 spots for SRR12483304/SRR12483304.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159138 ("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: 00:11:25 13717587 reads; of these: 13717587 (100.00%) were paired; of these: 1125660 (8.21%) aligned concordantly 0 times 10916198 (79.58%) aligned concordantly exactly 1 time 1675729 (12.22%) aligned concordantly >1 times ---- 1125660 pairs aligned concordantly 0 times; of these: 814017 (72.31%) aligned discordantly 1 time ---- 311643 pairs aligned 0 times concordantly or discordantly; of these: 623286 mates make up the pairs; of these: 229059 (36.75%) aligned 0 times 182181 (29.23%) aligned exactly 1 time 212046 (34.02%) aligned >1 times 99.17% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 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] 235972 / 13392636 = 0.0176 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 17:56:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.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 17:56:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:56:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:56:36: 1000000 INFO @ Wed, 08 Dec 2021 17:56:41: 2000000 INFO @ Wed, 08 Dec 2021 17:56:47: 3000000 INFO @ Wed, 08 Dec 2021 17:56:53: 4000000 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 17:56:58: 5000000 INFO @ Wed, 08 Dec 2021 17:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.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 17:56:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:56:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:57:04: 6000000 INFO @ Wed, 08 Dec 2021 17:57:05: 1000000 INFO @ Wed, 08 Dec 2021 17:57:10: 7000000 INFO @ Wed, 08 Dec 2021 17:57:11: 2000000 INFO @ Wed, 08 Dec 2021 17:57:16: 8000000 INFO @ Wed, 08 Dec 2021 17:57:17: 3000000 INFO @ Wed, 08 Dec 2021 17:57:21: 9000000 INFO @ Wed, 08 Dec 2021 17:57:23: 4000000 INFO @ Wed, 08 Dec 2021 17:57:27: 10000000 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 17:57:29: 5000000 INFO @ Wed, 08 Dec 2021 17:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.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 17:57:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:57:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:57:33: 11000000 INFO @ Wed, 08 Dec 2021 17:57:35: 1000000 INFO @ Wed, 08 Dec 2021 17:57:35: 6000000 INFO @ Wed, 08 Dec 2021 17:57:38: 12000000 INFO @ Wed, 08 Dec 2021 17:57:40: 2000000 INFO @ Wed, 08 Dec 2021 17:57:41: 7000000 INFO @ Wed, 08 Dec 2021 17:57:44: 13000000 INFO @ Wed, 08 Dec 2021 17:57:45: 3000000 INFO @ Wed, 08 Dec 2021 17:57:47: 8000000 INFO @ Wed, 08 Dec 2021 17:57:50: 14000000 INFO @ Wed, 08 Dec 2021 17:57:50: 4000000 INFO @ Wed, 08 Dec 2021 17:57:52: 9000000 INFO @ Wed, 08 Dec 2021 17:57:55: 15000000 INFO @ Wed, 08 Dec 2021 17:57:56: 5000000 INFO @ Wed, 08 Dec 2021 17:57:58: 10000000 INFO @ Wed, 08 Dec 2021 17:58:01: 6000000 INFO @ Wed, 08 Dec 2021 17:58:01: 16000000 INFO @ Wed, 08 Dec 2021 17:58:04: 11000000 INFO @ Wed, 08 Dec 2021 17:58:06: 7000000 INFO @ Wed, 08 Dec 2021 17:58:07: 17000000 INFO @ Wed, 08 Dec 2021 17:58:10: 12000000 INFO @ Wed, 08 Dec 2021 17:58:11: 8000000 INFO @ Wed, 08 Dec 2021 17:58:13: 18000000 INFO @ Wed, 08 Dec 2021 17:58:15: 13000000 INFO @ Wed, 08 Dec 2021 17:58:16: 9000000 INFO @ Wed, 08 Dec 2021 17:58:18: 19000000 INFO @ Wed, 08 Dec 2021 17:58:21: 14000000 INFO @ Wed, 08 Dec 2021 17:58:21: 10000000 INFO @ Wed, 08 Dec 2021 17:58:24: 20000000 INFO @ Wed, 08 Dec 2021 17:58:27: 11000000 INFO @ Wed, 08 Dec 2021 17:58:27: 15000000 INFO @ Wed, 08 Dec 2021 17:58:30: 21000000 INFO @ Wed, 08 Dec 2021 17:58:32: 12000000 INFO @ Wed, 08 Dec 2021 17:58:33: 16000000 INFO @ Wed, 08 Dec 2021 17:58:36: 22000000 INFO @ Wed, 08 Dec 2021 17:58:37: 13000000 INFO @ Wed, 08 Dec 2021 17:58:39: 17000000 INFO @ Wed, 08 Dec 2021 17:58:42: 23000000 INFO @ Wed, 08 Dec 2021 17:58:42: 14000000 INFO @ Wed, 08 Dec 2021 17:58:45: 18000000 INFO @ Wed, 08 Dec 2021 17:58:47: 15000000 INFO @ Wed, 08 Dec 2021 17:58:48: 24000000 INFO @ Wed, 08 Dec 2021 17:58:51: 19000000 INFO @ Wed, 08 Dec 2021 17:58:53: 16000000 INFO @ Wed, 08 Dec 2021 17:58:54: 25000000 INFO @ Wed, 08 Dec 2021 17:58:57: 20000000 INFO @ Wed, 08 Dec 2021 17:58:58: 17000000 INFO @ Wed, 08 Dec 2021 17:59:00: 26000000 INFO @ Wed, 08 Dec 2021 17:59:03: 21000000 INFO @ Wed, 08 Dec 2021 17:59:03: 18000000 INFO @ Wed, 08 Dec 2021 17:59:04: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 17:59:04: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 17:59:04: #1 total tags in treatment: 12365306 INFO @ Wed, 08 Dec 2021 17:59:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:59:04: #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 17:59:04: #1 tags after filtering in treatment: 11527622 INFO @ Wed, 08 Dec 2021 17:59:04: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:59:04: #1 finished! INFO @ Wed, 08 Dec 2021 17:59:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:59:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:59:05: #2 number of paired peaks: 359 WARNING @ Wed, 08 Dec 2021 17:59:05: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Wed, 08 Dec 2021 17:59:05: start model_add_line... INFO @ Wed, 08 Dec 2021 17:59:05: start X-correlation... INFO @ Wed, 08 Dec 2021 17:59:05: end of X-cor INFO @ Wed, 08 Dec 2021 17:59:05: #2 finished! INFO @ Wed, 08 Dec 2021 17:59:05: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 17:59:05: #2 alternative fragment length(s) may be 4,155,166 bps INFO @ Wed, 08 Dec 2021 17:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.05_model.r INFO @ Wed, 08 Dec 2021 17:59:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:59:08: 19000000 INFO @ Wed, 08 Dec 2021 17:59:09: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:59:13: 20000000 INFO @ Wed, 08 Dec 2021 17:59:15: 23000000 INFO @ Wed, 08 Dec 2021 17:59:18: 21000000 INFO @ Wed, 08 Dec 2021 17:59:20: 24000000 INFO @ Wed, 08 Dec 2021 17:59:24: 22000000 INFO @ Wed, 08 Dec 2021 17:59:26: 25000000 INFO @ Wed, 08 Dec 2021 17:59:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:59:29: 23000000 INFO @ Wed, 08 Dec 2021 17:59:32: 26000000 INFO @ Wed, 08 Dec 2021 17:59:34: 24000000 INFO @ Wed, 08 Dec 2021 17:59:36: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 17:59:36: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 17:59:36: #1 total tags in treatment: 12365306 INFO @ Wed, 08 Dec 2021 17:59:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:59:36: #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 17:59:36: #1 tags after filtering in treatment: 11527622 INFO @ Wed, 08 Dec 2021 17:59:36: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:59:36: #1 finished! INFO @ Wed, 08 Dec 2021 17:59:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:59:37: #2 number of paired peaks: 359 WARNING @ Wed, 08 Dec 2021 17:59:37: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Wed, 08 Dec 2021 17:59:37: start model_add_line... INFO @ Wed, 08 Dec 2021 17:59:37: start X-correlation... INFO @ Wed, 08 Dec 2021 17:59:37: end of X-cor INFO @ Wed, 08 Dec 2021 17:59:37: #2 finished! INFO @ Wed, 08 Dec 2021 17:59:37: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 17:59:37: #2 alternative fragment length(s) may be 4,155,166 bps INFO @ Wed, 08 Dec 2021 17:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.10_model.r INFO @ Wed, 08 Dec 2021 17:59:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:59:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:59:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:59:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.05_summits.bed INFO @ Wed, 08 Dec 2021 17:59:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (357 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:59:39: 25000000 INFO @ Wed, 08 Dec 2021 17:59:44: 26000000 INFO @ Wed, 08 Dec 2021 17:59:47: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 17:59:47: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 17:59:47: #1 total tags in treatment: 12365306 INFO @ Wed, 08 Dec 2021 17:59:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:59:47: #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 17:59:47: #1 tags after filtering in treatment: 11527622 INFO @ Wed, 08 Dec 2021 17:59:47: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:59:47: #1 finished! INFO @ Wed, 08 Dec 2021 17:59:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:59:48: #2 number of paired peaks: 359 WARNING @ Wed, 08 Dec 2021 17:59:48: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Wed, 08 Dec 2021 17:59:48: start model_add_line... INFO @ Wed, 08 Dec 2021 17:59:48: start X-correlation... INFO @ Wed, 08 Dec 2021 17:59:48: end of X-cor INFO @ Wed, 08 Dec 2021 17:59:48: #2 finished! INFO @ Wed, 08 Dec 2021 17:59:48: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 17:59:48: #2 alternative fragment length(s) may be 4,155,166 bps INFO @ Wed, 08 Dec 2021 17:59:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.20_model.r INFO @ Wed, 08 Dec 2021 17:59:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:59:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:59:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.10_summits.bed INFO @ Wed, 08 Dec 2021 18:00:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:00:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:00:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976700/SRX8976700.20_summits.bed INFO @ Wed, 08 Dec 2021 18:00:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 5 millis CompletedMACS2peakCalling