Job ID = 14158783 SRX = SRX8976707 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11030633 spots for SRR12483311/SRR12483311.sra Written 11030633 spots for SRR12483311/SRR12483311.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159196 ("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: 00:10:44 11030633 reads; of these: 11030633 (100.00%) were paired; of these: 1995666 (18.09%) aligned concordantly 0 times 7097140 (64.34%) aligned concordantly exactly 1 time 1937827 (17.57%) aligned concordantly >1 times ---- 1995666 pairs aligned concordantly 0 times; of these: 1309600 (65.62%) aligned discordantly 1 time ---- 686066 pairs aligned 0 times concordantly or discordantly; of these: 1372132 mates make up the pairs; of these: 509707 (37.15%) aligned 0 times 338152 (24.64%) aligned exactly 1 time 524273 (38.21%) aligned >1 times 97.69% overall alignment rate Time searching: 00:10:44 Overall time: 00:10:44 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] 3236828 / 10339450 = 0.3131 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 18:08:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.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 18:08:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:08:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:08:23: 1000000 INFO @ Wed, 08 Dec 2021 18:08:28: 2000000 INFO @ Wed, 08 Dec 2021 18:08:32: 3000000 INFO @ Wed, 08 Dec 2021 18:08:36: 4000000 INFO @ Wed, 08 Dec 2021 18:08:40: 5000000 INFO @ Wed, 08 Dec 2021 18:08:45: 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 18:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.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 18:08:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:08:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:08:49: 7000000 INFO @ Wed, 08 Dec 2021 18:08:54: 8000000 INFO @ Wed, 08 Dec 2021 18:08:54: 1000000 INFO @ Wed, 08 Dec 2021 18:08:58: 9000000 INFO @ Wed, 08 Dec 2021 18:08:58: 2000000 INFO @ Wed, 08 Dec 2021 18:09:03: 10000000 INFO @ Wed, 08 Dec 2021 18:09:03: 3000000 INFO @ Wed, 08 Dec 2021 18:09:07: 11000000 INFO @ Wed, 08 Dec 2021 18:09:07: 4000000 INFO @ Wed, 08 Dec 2021 18:09:11: 12000000 INFO @ Wed, 08 Dec 2021 18:09:12: 5000000 INFO @ Wed, 08 Dec 2021 18:09:16: 13000000 INFO @ Wed, 08 Dec 2021 18:09:16: 6000000 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 18:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.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 18:09:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:09:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:09:20: 14000000 INFO @ Wed, 08 Dec 2021 18:09:21: 7000000 INFO @ Wed, 08 Dec 2021 18:09:25: 1000000 INFO @ Wed, 08 Dec 2021 18:09:25: 15000000 INFO @ Wed, 08 Dec 2021 18:09:25: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:09:25: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:09:25: #1 total tags in treatment: 6100715 INFO @ Wed, 08 Dec 2021 18:09:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:09:25: #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 18:09:25: #1 tags after filtering in treatment: 5443320 INFO @ Wed, 08 Dec 2021 18:09:25: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:09:25: #1 finished! INFO @ Wed, 08 Dec 2021 18:09:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:09:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:09:26: 8000000 INFO @ Wed, 08 Dec 2021 18:09:26: #2 number of paired peaks: 855 WARNING @ Wed, 08 Dec 2021 18:09:26: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Wed, 08 Dec 2021 18:09:26: start model_add_line... INFO @ Wed, 08 Dec 2021 18:09:26: start X-correlation... INFO @ Wed, 08 Dec 2021 18:09:26: end of X-cor INFO @ Wed, 08 Dec 2021 18:09:26: #2 finished! INFO @ Wed, 08 Dec 2021 18:09:26: #2 predicted fragment length is 164 bps INFO @ Wed, 08 Dec 2021 18:09:26: #2 alternative fragment length(s) may be 164 bps INFO @ Wed, 08 Dec 2021 18:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.05_model.r INFO @ Wed, 08 Dec 2021 18:09:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:09:30: 2000000 INFO @ Wed, 08 Dec 2021 18:09:30: 9000000 INFO @ Wed, 08 Dec 2021 18:09:35: 10000000 INFO @ Wed, 08 Dec 2021 18:09:36: 3000000 INFO @ Wed, 08 Dec 2021 18:09:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:09:40: 11000000 INFO @ Wed, 08 Dec 2021 18:09:41: 4000000 INFO @ Wed, 08 Dec 2021 18:09:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:09:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:09:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.05_summits.bed INFO @ Wed, 08 Dec 2021 18:09:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (713 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:09:44: 12000000 INFO @ Wed, 08 Dec 2021 18:09:46: 5000000 INFO @ Wed, 08 Dec 2021 18:09:49: 13000000 INFO @ Wed, 08 Dec 2021 18:09:52: 6000000 INFO @ Wed, 08 Dec 2021 18:09:54: 14000000 INFO @ Wed, 08 Dec 2021 18:09:57: 7000000 INFO @ Wed, 08 Dec 2021 18:09:58: 15000000 INFO @ Wed, 08 Dec 2021 18:09:59: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:09:59: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:09:59: #1 total tags in treatment: 6100715 INFO @ Wed, 08 Dec 2021 18:09:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:09:59: #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 18:09:59: #1 tags after filtering in treatment: 5443320 INFO @ Wed, 08 Dec 2021 18:09:59: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:09:59: #1 finished! INFO @ Wed, 08 Dec 2021 18:09:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:09:59: #2 number of paired peaks: 855 WARNING @ Wed, 08 Dec 2021 18:09:59: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Wed, 08 Dec 2021 18:09:59: start model_add_line... INFO @ Wed, 08 Dec 2021 18:09:59: start X-correlation... INFO @ Wed, 08 Dec 2021 18:09:59: end of X-cor INFO @ Wed, 08 Dec 2021 18:09:59: #2 finished! INFO @ Wed, 08 Dec 2021 18:09:59: #2 predicted fragment length is 164 bps INFO @ Wed, 08 Dec 2021 18:09:59: #2 alternative fragment length(s) may be 164 bps INFO @ Wed, 08 Dec 2021 18:09:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.10_model.r INFO @ Wed, 08 Dec 2021 18:09:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:09:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:10:02: 8000000 INFO @ Wed, 08 Dec 2021 18:10:07: 9000000 INFO @ Wed, 08 Dec 2021 18:10:12: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:10:12: 10000000 INFO @ Wed, 08 Dec 2021 18:10:17: 11000000 INFO @ Wed, 08 Dec 2021 18:10:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:10:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:10:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.10_summits.bed INFO @ Wed, 08 Dec 2021 18:10:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (421 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:10:22: 12000000 INFO @ Wed, 08 Dec 2021 18:10:28: 13000000 INFO @ Wed, 08 Dec 2021 18:10:33: 14000000 INFO @ Wed, 08 Dec 2021 18:10:38: 15000000 INFO @ Wed, 08 Dec 2021 18:10:38: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:10:38: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:10:38: #1 total tags in treatment: 6100715 INFO @ Wed, 08 Dec 2021 18:10:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:10:38: #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 18:10:38: #1 tags after filtering in treatment: 5443320 INFO @ Wed, 08 Dec 2021 18:10:38: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:10:38: #1 finished! INFO @ Wed, 08 Dec 2021 18:10:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:10:39: #2 number of paired peaks: 855 WARNING @ Wed, 08 Dec 2021 18:10:39: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Wed, 08 Dec 2021 18:10:39: start model_add_line... INFO @ Wed, 08 Dec 2021 18:10:39: start X-correlation... INFO @ Wed, 08 Dec 2021 18:10:39: end of X-cor INFO @ Wed, 08 Dec 2021 18:10:39: #2 finished! INFO @ Wed, 08 Dec 2021 18:10:39: #2 predicted fragment length is 164 bps INFO @ Wed, 08 Dec 2021 18:10:39: #2 alternative fragment length(s) may be 164 bps INFO @ Wed, 08 Dec 2021 18:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.20_model.r INFO @ Wed, 08 Dec 2021 18:10:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:10:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:10:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976707/SRX8976707.20_summits.bed INFO @ Wed, 08 Dec 2021 18:10:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (266 records, 4 fields): 2 millis CompletedMACS2peakCalling