Job ID = 14159196 SRX = SRX8976707 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:36 11030633 reads; of these: 11030633 (100.00%) were paired; of these: 1995567 (18.09%) aligned concordantly 0 times 7097100 (64.34%) aligned concordantly exactly 1 time 1937966 (17.57%) aligned concordantly >1 times ---- 1995567 pairs aligned concordantly 0 times; of these: 1309667 (65.63%) aligned discordantly 1 time ---- 685900 pairs aligned 0 times concordantly or discordantly; of these: 1371800 mates make up the pairs; of these: 509427 (37.14%) aligned 0 times 338091 (24.65%) aligned exactly 1 time 524282 (38.22%) aligned >1 times 97.69% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 3236939 / 10339616 = 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 20:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 20:23:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:23:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:23:06: 1000000 INFO @ Wed, 08 Dec 2021 20:23:10: 2000000 INFO @ Wed, 08 Dec 2021 20:23:15: 3000000 INFO @ Wed, 08 Dec 2021 20:23:19: 4000000 INFO @ Wed, 08 Dec 2021 20:23:23: 5000000 INFO @ Wed, 08 Dec 2021 20:23:28: 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 20:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 20:23:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:23:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:23:32: 7000000 INFO @ Wed, 08 Dec 2021 20:23:37: 8000000 INFO @ Wed, 08 Dec 2021 20:23:37: 1000000 INFO @ Wed, 08 Dec 2021 20:23:41: 9000000 INFO @ Wed, 08 Dec 2021 20:23:43: 2000000 INFO @ Wed, 08 Dec 2021 20:23:46: 10000000 INFO @ Wed, 08 Dec 2021 20:23:48: 3000000 INFO @ Wed, 08 Dec 2021 20:23:51: 11000000 INFO @ Wed, 08 Dec 2021 20:23:54: 4000000 INFO @ Wed, 08 Dec 2021 20:23:55: 12000000 INFO @ Wed, 08 Dec 2021 20:23:59: 5000000 INFO @ Wed, 08 Dec 2021 20:24:00: 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 20:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 20:24:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:24:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:24:04: 6000000 INFO @ Wed, 08 Dec 2021 20:24:04: 14000000 INFO @ Wed, 08 Dec 2021 20:24:07: 1000000 INFO @ Wed, 08 Dec 2021 20:24:09: 15000000 INFO @ Wed, 08 Dec 2021 20:24:10: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:24:10: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:24:10: #1 total tags in treatment: 6100727 INFO @ Wed, 08 Dec 2021 20:24:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:24:10: #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 20:24:10: #1 tags after filtering in treatment: 5443346 INFO @ Wed, 08 Dec 2021 20:24:10: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:24:10: #1 finished! INFO @ Wed, 08 Dec 2021 20:24:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:24:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:24:10: 7000000 INFO @ Wed, 08 Dec 2021 20:24:10: #2 number of paired peaks: 854 WARNING @ Wed, 08 Dec 2021 20:24:10: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Wed, 08 Dec 2021 20:24:10: start model_add_line... INFO @ Wed, 08 Dec 2021 20:24:10: start X-correlation... INFO @ Wed, 08 Dec 2021 20:24:10: end of X-cor INFO @ Wed, 08 Dec 2021 20:24:10: #2 finished! INFO @ Wed, 08 Dec 2021 20:24:10: #2 predicted fragment length is 165 bps INFO @ Wed, 08 Dec 2021 20:24:10: #2 alternative fragment length(s) may be 165 bps INFO @ Wed, 08 Dec 2021 20:24:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.05_model.r INFO @ Wed, 08 Dec 2021 20:24:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:24:13: 2000000 INFO @ Wed, 08 Dec 2021 20:24:16: 8000000 INFO @ Wed, 08 Dec 2021 20:24:18: 3000000 INFO @ Wed, 08 Dec 2021 20:24:21: 9000000 INFO @ Wed, 08 Dec 2021 20:24:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:24:24: 4000000 INFO @ Wed, 08 Dec 2021 20:24:27: 10000000 INFO @ Wed, 08 Dec 2021 20:24:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:24:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:24:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.05_summits.bed INFO @ Wed, 08 Dec 2021 20:24:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (722 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:24:30: 5000000 INFO @ Wed, 08 Dec 2021 20:24:33: 11000000 INFO @ Wed, 08 Dec 2021 20:24:35: 6000000 INFO @ Wed, 08 Dec 2021 20:24:38: 12000000 INFO @ Wed, 08 Dec 2021 20:24:41: 7000000 INFO @ Wed, 08 Dec 2021 20:24:43: 13000000 INFO @ Wed, 08 Dec 2021 20:24:46: 8000000 INFO @ Wed, 08 Dec 2021 20:24:49: 14000000 INFO @ Wed, 08 Dec 2021 20:24:52: 9000000 INFO @ Wed, 08 Dec 2021 20:24:54: 15000000 INFO @ Wed, 08 Dec 2021 20:24:55: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:24:55: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:24:55: #1 total tags in treatment: 6100727 INFO @ Wed, 08 Dec 2021 20:24:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:24:55: #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 20:24:55: #1 tags after filtering in treatment: 5443346 INFO @ Wed, 08 Dec 2021 20:24:55: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:24:55: #1 finished! INFO @ Wed, 08 Dec 2021 20:24:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:24:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:24:55: #2 number of paired peaks: 854 WARNING @ Wed, 08 Dec 2021 20:24:55: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Wed, 08 Dec 2021 20:24:55: start model_add_line... INFO @ Wed, 08 Dec 2021 20:24:55: start X-correlation... INFO @ Wed, 08 Dec 2021 20:24:55: end of X-cor INFO @ Wed, 08 Dec 2021 20:24:55: #2 finished! INFO @ Wed, 08 Dec 2021 20:24:55: #2 predicted fragment length is 165 bps INFO @ Wed, 08 Dec 2021 20:24:55: #2 alternative fragment length(s) may be 165 bps INFO @ Wed, 08 Dec 2021 20:24:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.10_model.r INFO @ Wed, 08 Dec 2021 20:24:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:24:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:24:57: 10000000 INFO @ Wed, 08 Dec 2021 20:25:02: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:25:07: 12000000 INFO @ Wed, 08 Dec 2021 20:25:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:25:12: 13000000 INFO @ Wed, 08 Dec 2021 20:25:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:25:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:25:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.10_summits.bed INFO @ Wed, 08 Dec 2021 20:25:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:25:18: 14000000 INFO @ Wed, 08 Dec 2021 20:25:23: 15000000 INFO @ Wed, 08 Dec 2021 20:25:23: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:25:23: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:25:23: #1 total tags in treatment: 6100727 INFO @ Wed, 08 Dec 2021 20:25:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:25:23: #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 20:25:23: #1 tags after filtering in treatment: 5443346 INFO @ Wed, 08 Dec 2021 20:25:23: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:25:23: #1 finished! INFO @ Wed, 08 Dec 2021 20:25:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:25:24: #2 number of paired peaks: 854 WARNING @ Wed, 08 Dec 2021 20:25:24: Fewer paired peaks (854) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 854 pairs to build model! INFO @ Wed, 08 Dec 2021 20:25:24: start model_add_line... INFO @ Wed, 08 Dec 2021 20:25:24: start X-correlation... INFO @ Wed, 08 Dec 2021 20:25:24: end of X-cor INFO @ Wed, 08 Dec 2021 20:25:24: #2 finished! INFO @ Wed, 08 Dec 2021 20:25:24: #2 predicted fragment length is 165 bps INFO @ Wed, 08 Dec 2021 20:25:24: #2 alternative fragment length(s) may be 165 bps INFO @ Wed, 08 Dec 2021 20:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.20_model.r INFO @ Wed, 08 Dec 2021 20:25:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:25:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:25:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:25:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:25:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:25:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976707/SRX8976707.20_summits.bed INFO @ Wed, 08 Dec 2021 20:25:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 1 millis CompletedMACS2peakCalling