Job ID = 14158857 SRX = SRX10342591 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: 00:13:14 19971878 reads; of these: 19971878 (100.00%) were paired; of these: 8984956 (44.99%) aligned concordantly 0 times 9552856 (47.83%) aligned concordantly exactly 1 time 1434066 (7.18%) aligned concordantly >1 times ---- 8984956 pairs aligned concordantly 0 times; of these: 5108820 (56.86%) aligned discordantly 1 time ---- 3876136 pairs aligned 0 times concordantly or discordantly; of these: 7752272 mates make up the pairs; of these: 5900982 (76.12%) aligned 0 times 759384 (9.80%) aligned exactly 1 time 1091906 (14.08%) aligned >1 times 85.23% overall alignment rate Time searching: 00:13:14 Overall time: 00:13:14 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] 6780789 / 16089715 = 0.4214 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 18:28:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.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 18:28:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:28:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:28:53: 1000000 INFO @ Wed, 08 Dec 2021 18:28:58: 2000000 INFO @ Wed, 08 Dec 2021 18:29:02: 3000000 INFO @ Wed, 08 Dec 2021 18:29:06: 4000000 INFO @ Wed, 08 Dec 2021 18:29:11: 5000000 INFO @ Wed, 08 Dec 2021 18:29:15: 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 18:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.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 18:29:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:29:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:29:20: 7000000 INFO @ Wed, 08 Dec 2021 18:29:23: 1000000 INFO @ Wed, 08 Dec 2021 18:29:24: 8000000 INFO @ Wed, 08 Dec 2021 18:29:27: 2000000 INFO @ Wed, 08 Dec 2021 18:29:29: 9000000 INFO @ Wed, 08 Dec 2021 18:29:31: 3000000 INFO @ Wed, 08 Dec 2021 18:29:33: 10000000 INFO @ Wed, 08 Dec 2021 18:29:35: 4000000 INFO @ Wed, 08 Dec 2021 18:29:38: 11000000 INFO @ Wed, 08 Dec 2021 18:29:39: 5000000 INFO @ Wed, 08 Dec 2021 18:29:42: 12000000 INFO @ Wed, 08 Dec 2021 18:29:43: 6000000 INFO @ Wed, 08 Dec 2021 18:29:47: 7000000 INFO @ Wed, 08 Dec 2021 18:29:47: 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 18:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.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 18:29:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:29:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:29:51: 8000000 INFO @ Wed, 08 Dec 2021 18:29:52: 14000000 INFO @ Wed, 08 Dec 2021 18:29:55: 9000000 INFO @ Wed, 08 Dec 2021 18:29:55: 1000000 INFO @ Wed, 08 Dec 2021 18:29:56: 15000000 INFO @ Wed, 08 Dec 2021 18:29:59: 10000000 INFO @ Wed, 08 Dec 2021 18:30:01: 16000000 INFO @ Wed, 08 Dec 2021 18:30:01: 2000000 INFO @ Wed, 08 Dec 2021 18:30:03: 11000000 INFO @ Wed, 08 Dec 2021 18:30:05: 17000000 INFO @ Wed, 08 Dec 2021 18:30:07: 3000000 INFO @ Wed, 08 Dec 2021 18:30:07: 12000000 INFO @ Wed, 08 Dec 2021 18:30:10: 18000000 INFO @ Wed, 08 Dec 2021 18:30:11: 13000000 INFO @ Wed, 08 Dec 2021 18:30:13: 4000000 INFO @ Wed, 08 Dec 2021 18:30:15: 19000000 INFO @ Wed, 08 Dec 2021 18:30:15: 14000000 INFO @ Wed, 08 Dec 2021 18:30:19: 5000000 INFO @ Wed, 08 Dec 2021 18:30:19: 15000000 INFO @ Wed, 08 Dec 2021 18:30:19: 20000000 INFO @ Wed, 08 Dec 2021 18:30:22: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:30:22: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:30:22: #1 total tags in treatment: 5988658 INFO @ Wed, 08 Dec 2021 18:30:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:30:22: #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 18:30:22: #1 tags after filtering in treatment: 5620218 INFO @ Wed, 08 Dec 2021 18:30:22: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:30:22: #1 finished! INFO @ Wed, 08 Dec 2021 18:30:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:30:22: #2 number of paired peaks: 677 WARNING @ Wed, 08 Dec 2021 18:30:22: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Wed, 08 Dec 2021 18:30:22: start model_add_line... INFO @ Wed, 08 Dec 2021 18:30:22: start X-correlation... INFO @ Wed, 08 Dec 2021 18:30:22: end of X-cor INFO @ Wed, 08 Dec 2021 18:30:22: #2 finished! INFO @ Wed, 08 Dec 2021 18:30:22: #2 predicted fragment length is 156 bps INFO @ Wed, 08 Dec 2021 18:30:22: #2 alternative fragment length(s) may be 4,156 bps INFO @ Wed, 08 Dec 2021 18:30:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.05_model.r INFO @ Wed, 08 Dec 2021 18:30:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:30:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:30:23: 16000000 INFO @ Wed, 08 Dec 2021 18:30:25: 6000000 INFO @ Wed, 08 Dec 2021 18:30:27: 17000000 INFO @ Wed, 08 Dec 2021 18:30:31: 7000000 INFO @ Wed, 08 Dec 2021 18:30:31: 18000000 INFO @ Wed, 08 Dec 2021 18:30:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:30:35: 19000000 INFO @ Wed, 08 Dec 2021 18:30:37: 8000000 INFO @ Wed, 08 Dec 2021 18:30:39: 20000000 INFO @ Wed, 08 Dec 2021 18:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.05_summits.bed INFO @ Wed, 08 Dec 2021 18:30:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1419 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:30:41: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:30:41: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:30:41: #1 total tags in treatment: 5988658 INFO @ Wed, 08 Dec 2021 18:30:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:30:41: #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 18:30:41: #1 tags after filtering in treatment: 5620218 INFO @ Wed, 08 Dec 2021 18:30:41: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:30:41: #1 finished! INFO @ Wed, 08 Dec 2021 18:30:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:30:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:30:42: #2 number of paired peaks: 677 WARNING @ Wed, 08 Dec 2021 18:30:42: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Wed, 08 Dec 2021 18:30:42: start model_add_line... INFO @ Wed, 08 Dec 2021 18:30:42: start X-correlation... INFO @ Wed, 08 Dec 2021 18:30:42: end of X-cor INFO @ Wed, 08 Dec 2021 18:30:42: #2 finished! INFO @ Wed, 08 Dec 2021 18:30:42: #2 predicted fragment length is 156 bps INFO @ Wed, 08 Dec 2021 18:30:42: #2 alternative fragment length(s) may be 4,156 bps INFO @ Wed, 08 Dec 2021 18:30:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.10_model.r INFO @ Wed, 08 Dec 2021 18:30:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:30:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:30:43: 9000000 INFO @ Wed, 08 Dec 2021 18:30:49: 10000000 INFO @ Wed, 08 Dec 2021 18:30:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:30:55: 11000000 INFO @ Wed, 08 Dec 2021 18:30:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:30:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.10_summits.bed INFO @ Wed, 08 Dec 2021 18:30:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:31:00: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:31:06: 13000000 INFO @ Wed, 08 Dec 2021 18:31:12: 14000000 INFO @ Wed, 08 Dec 2021 18:31:18: 15000000 INFO @ Wed, 08 Dec 2021 18:31:24: 16000000 INFO @ Wed, 08 Dec 2021 18:31:30: 17000000 INFO @ Wed, 08 Dec 2021 18:31:36: 18000000 INFO @ Wed, 08 Dec 2021 18:31:42: 19000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:31:47: 20000000 INFO @ Wed, 08 Dec 2021 18:31:50: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:31:50: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:31:50: #1 total tags in treatment: 5988658 INFO @ Wed, 08 Dec 2021 18:31:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:31:50: #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 18:31:50: #1 tags after filtering in treatment: 5620218 INFO @ Wed, 08 Dec 2021 18:31:50: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:31:50: #1 finished! INFO @ Wed, 08 Dec 2021 18:31:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:31:51: #2 number of paired peaks: 677 WARNING @ Wed, 08 Dec 2021 18:31:51: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Wed, 08 Dec 2021 18:31:51: start model_add_line... INFO @ Wed, 08 Dec 2021 18:31:51: start X-correlation... INFO @ Wed, 08 Dec 2021 18:31:51: end of X-cor INFO @ Wed, 08 Dec 2021 18:31:51: #2 finished! INFO @ Wed, 08 Dec 2021 18:31:51: #2 predicted fragment length is 156 bps INFO @ Wed, 08 Dec 2021 18:31:51: #2 alternative fragment length(s) may be 4,156 bps INFO @ Wed, 08 Dec 2021 18:31:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.20_model.r INFO @ Wed, 08 Dec 2021 18:31:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:31:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:32:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342591/SRX10342591.20_summits.bed INFO @ Wed, 08 Dec 2021 18:32:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling