Job ID = 14158504 SRX = SRX8976704 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12141993 spots for SRR12483308/SRR12483308.sra Written 12141993 spots for SRR12483308/SRR12483308.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159140 ("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: 00:10:08 12141993 reads; of these: 12141993 (100.00%) were paired; of these: 989826 (8.15%) aligned concordantly 0 times 9657439 (79.54%) aligned concordantly exactly 1 time 1494728 (12.31%) aligned concordantly >1 times ---- 989826 pairs aligned concordantly 0 times; of these: 695890 (70.30%) aligned discordantly 1 time ---- 293936 pairs aligned 0 times concordantly or discordantly; of these: 587872 mates make up the pairs; of these: 244417 (41.58%) aligned 0 times 160644 (27.33%) aligned exactly 1 time 182811 (31.10%) aligned >1 times 98.99% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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] 199224 / 11837317 = 0.0168 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 17:57:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.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 17:57:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:57:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:57:09: 1000000 INFO @ Wed, 08 Dec 2021 17:57:14: 2000000 INFO @ Wed, 08 Dec 2021 17:57:19: 3000000 INFO @ Wed, 08 Dec 2021 17:57:25: 4000000 INFO @ Wed, 08 Dec 2021 17:57:30: 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 @ Wed, 08 Dec 2021 17:57:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.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 17:57:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:57:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:57:35: 6000000 INFO @ Wed, 08 Dec 2021 17:57:40: 1000000 INFO @ Wed, 08 Dec 2021 17:57:41: 7000000 INFO @ Wed, 08 Dec 2021 17:57:46: 2000000 INFO @ Wed, 08 Dec 2021 17:57:47: 8000000 INFO @ Wed, 08 Dec 2021 17:57:52: 3000000 INFO @ Wed, 08 Dec 2021 17:57:53: 9000000 INFO @ Wed, 08 Dec 2021 17:57:59: 4000000 INFO @ Wed, 08 Dec 2021 17:58:00: 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 17:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.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 17:58:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:58:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:58:05: 5000000 INFO @ Wed, 08 Dec 2021 17:58:06: 11000000 INFO @ Wed, 08 Dec 2021 17:58:10: 1000000 INFO @ Wed, 08 Dec 2021 17:58:11: 6000000 INFO @ Wed, 08 Dec 2021 17:58:12: 12000000 INFO @ Wed, 08 Dec 2021 17:58:17: 2000000 INFO @ Wed, 08 Dec 2021 17:58:18: 7000000 INFO @ Wed, 08 Dec 2021 17:58:19: 13000000 INFO @ Wed, 08 Dec 2021 17:58:23: 3000000 INFO @ Wed, 08 Dec 2021 17:58:24: 8000000 INFO @ Wed, 08 Dec 2021 17:58:25: 14000000 INFO @ Wed, 08 Dec 2021 17:58:29: 4000000 INFO @ Wed, 08 Dec 2021 17:58:30: 9000000 INFO @ Wed, 08 Dec 2021 17:58:31: 15000000 INFO @ Wed, 08 Dec 2021 17:58:35: 5000000 INFO @ Wed, 08 Dec 2021 17:58:37: 10000000 INFO @ Wed, 08 Dec 2021 17:58:38: 16000000 INFO @ Wed, 08 Dec 2021 17:58:42: 6000000 INFO @ Wed, 08 Dec 2021 17:58:43: 11000000 INFO @ Wed, 08 Dec 2021 17:58:44: 17000000 INFO @ Wed, 08 Dec 2021 17:58:48: 7000000 INFO @ Wed, 08 Dec 2021 17:58:50: 12000000 INFO @ Wed, 08 Dec 2021 17:58:50: 18000000 INFO @ Wed, 08 Dec 2021 17:58:54: 8000000 INFO @ Wed, 08 Dec 2021 17:58:56: 13000000 INFO @ Wed, 08 Dec 2021 17:58:57: 19000000 INFO @ Wed, 08 Dec 2021 17:59:00: 9000000 INFO @ Wed, 08 Dec 2021 17:59:02: 14000000 INFO @ Wed, 08 Dec 2021 17:59:03: 20000000 INFO @ Wed, 08 Dec 2021 17:59:07: 10000000 INFO @ Wed, 08 Dec 2021 17:59:09: 15000000 INFO @ Wed, 08 Dec 2021 17:59:10: 21000000 INFO @ Wed, 08 Dec 2021 17:59:13: 11000000 INFO @ Wed, 08 Dec 2021 17:59:15: 16000000 INFO @ Wed, 08 Dec 2021 17:59:16: 22000000 INFO @ Wed, 08 Dec 2021 17:59:19: 12000000 INFO @ Wed, 08 Dec 2021 17:59:22: 17000000 INFO @ Wed, 08 Dec 2021 17:59:22: 23000000 INFO @ Wed, 08 Dec 2021 17:59:25: 13000000 INFO @ Wed, 08 Dec 2021 17:59:26: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 17:59:26: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 17:59:26: #1 total tags in treatment: 10960341 INFO @ Wed, 08 Dec 2021 17:59:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:59:26: #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 17:59:27: #1 tags after filtering in treatment: 10307127 INFO @ Wed, 08 Dec 2021 17:59:27: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 17:59:27: #1 finished! INFO @ Wed, 08 Dec 2021 17:59:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:59:27: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 17:59:27: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 17:59:27: start model_add_line... INFO @ Wed, 08 Dec 2021 17:59:27: start X-correlation... INFO @ Wed, 08 Dec 2021 17:59:27: end of X-cor INFO @ Wed, 08 Dec 2021 17:59:27: #2 finished! INFO @ Wed, 08 Dec 2021 17:59:27: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 17:59:27: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 17:59:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.05_model.r INFO @ Wed, 08 Dec 2021 17:59:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:59:28: 18000000 INFO @ Wed, 08 Dec 2021 17:59:32: 14000000 INFO @ Wed, 08 Dec 2021 17:59:34: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:59:38: 15000000 INFO @ Wed, 08 Dec 2021 17:59:40: 20000000 INFO @ Wed, 08 Dec 2021 17:59:44: 16000000 INFO @ Wed, 08 Dec 2021 17:59:47: 21000000 INFO @ Wed, 08 Dec 2021 17:59:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:59:50: 17000000 INFO @ Wed, 08 Dec 2021 17:59:53: 22000000 INFO @ Wed, 08 Dec 2021 17:59:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:59:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:59:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.05_summits.bed INFO @ Wed, 08 Dec 2021 17:59:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:59:57: 18000000 INFO @ Wed, 08 Dec 2021 17:59:59: 23000000 INFO @ Wed, 08 Dec 2021 18:00:03: 19000000 INFO @ Wed, 08 Dec 2021 18:00:03: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:00:03: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:00:03: #1 total tags in treatment: 10960341 INFO @ Wed, 08 Dec 2021 18:00:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:00:03: #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 18:00:03: #1 tags after filtering in treatment: 10307127 INFO @ Wed, 08 Dec 2021 18:00:03: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:00:03: #1 finished! INFO @ Wed, 08 Dec 2021 18:00:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:00:04: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 18:00:04: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 18:00:04: start model_add_line... INFO @ Wed, 08 Dec 2021 18:00:04: start X-correlation... INFO @ Wed, 08 Dec 2021 18:00:04: end of X-cor INFO @ Wed, 08 Dec 2021 18:00:04: #2 finished! INFO @ Wed, 08 Dec 2021 18:00:04: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 18:00:04: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 18:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.10_model.r INFO @ Wed, 08 Dec 2021 18:00:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:00:09: 20000000 INFO @ Wed, 08 Dec 2021 18:00:15: 21000000 INFO @ Wed, 08 Dec 2021 18:00:20: 22000000 INFO @ Wed, 08 Dec 2021 18:00:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:00:26: 23000000 INFO @ Wed, 08 Dec 2021 18:00:29: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:00:29: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:00:29: #1 total tags in treatment: 10960341 INFO @ Wed, 08 Dec 2021 18:00:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:00:29: #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 18:00:30: #1 tags after filtering in treatment: 10307127 INFO @ Wed, 08 Dec 2021 18:00:30: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:00:30: #1 finished! INFO @ Wed, 08 Dec 2021 18:00:30: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:00:30: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 18:00:30: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 18:00:30: start model_add_line... INFO @ Wed, 08 Dec 2021 18:00:30: start X-correlation... INFO @ Wed, 08 Dec 2021 18:00:30: end of X-cor INFO @ Wed, 08 Dec 2021 18:00:30: #2 finished! INFO @ Wed, 08 Dec 2021 18:00:30: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 18:00:30: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 18:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.20_model.r INFO @ Wed, 08 Dec 2021 18:00:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:00:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.10_summits.bed INFO @ Wed, 08 Dec 2021 18:00:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (271 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:00:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:00:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:00:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:00:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976704/SRX8976704.20_summits.bed INFO @ Wed, 08 Dec 2021 18:00:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis CompletedMACS2peakCalling