Job ID = 14159340 SRX = SRX8976734 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: 00:11:27 14560532 reads; of these: 14560532 (100.00%) were paired; of these: 1045295 (7.18%) aligned concordantly 0 times 11762865 (80.79%) aligned concordantly exactly 1 time 1752372 (12.04%) aligned concordantly >1 times ---- 1045295 pairs aligned concordantly 0 times; of these: 746383 (71.40%) aligned discordantly 1 time ---- 298912 pairs aligned 0 times concordantly or discordantly; of these: 597824 mates make up the pairs; of these: 185686 (31.06%) aligned 0 times 195713 (32.74%) aligned exactly 1 time 216425 (36.20%) aligned >1 times 99.36% overall alignment rate Time searching: 00:11:28 Overall time: 00:11:28 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] 415483 / 14223780 = 0.0292 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 21:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.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 21:23:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:23:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:23:33: 1000000 INFO @ Wed, 08 Dec 2021 21:23:38: 2000000 INFO @ Wed, 08 Dec 2021 21:23:44: 3000000 INFO @ Wed, 08 Dec 2021 21:23:49: 4000000 INFO @ Wed, 08 Dec 2021 21:23:54: 5000000 INFO @ Wed, 08 Dec 2021 21:23:59: 6000000 INFO @ Wed, 08 Dec 2021 21:24:05: 7000000 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 21:24:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.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 21:24:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:24:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:24:10: 8000000 INFO @ Wed, 08 Dec 2021 21:24:14: 1000000 INFO @ Wed, 08 Dec 2021 21:24:16: 9000000 INFO @ Wed, 08 Dec 2021 21:24:19: 2000000 INFO @ Wed, 08 Dec 2021 21:24:22: 10000000 INFO @ Wed, 08 Dec 2021 21:24:25: 3000000 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 21:24:27: 11000000 INFO @ Wed, 08 Dec 2021 21:24:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.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 21:24:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:24:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:24:30: 4000000 INFO @ Wed, 08 Dec 2021 21:24:33: 12000000 INFO @ Wed, 08 Dec 2021 21:24:33: 1000000 INFO @ Wed, 08 Dec 2021 21:24:36: 5000000 INFO @ Wed, 08 Dec 2021 21:24:39: 13000000 INFO @ Wed, 08 Dec 2021 21:24:39: 2000000 INFO @ Wed, 08 Dec 2021 21:24:42: 6000000 INFO @ Wed, 08 Dec 2021 21:24:44: 14000000 INFO @ Wed, 08 Dec 2021 21:24:45: 3000000 INFO @ Wed, 08 Dec 2021 21:24:48: 7000000 INFO @ Wed, 08 Dec 2021 21:24:50: 15000000 INFO @ Wed, 08 Dec 2021 21:24:51: 4000000 INFO @ Wed, 08 Dec 2021 21:24:54: 8000000 INFO @ Wed, 08 Dec 2021 21:24:56: 5000000 INFO @ Wed, 08 Dec 2021 21:24:56: 16000000 INFO @ Wed, 08 Dec 2021 21:24:59: 9000000 INFO @ Wed, 08 Dec 2021 21:25:01: 6000000 INFO @ Wed, 08 Dec 2021 21:25:02: 17000000 INFO @ Wed, 08 Dec 2021 21:25:05: 10000000 INFO @ Wed, 08 Dec 2021 21:25:06: 7000000 INFO @ Wed, 08 Dec 2021 21:25:08: 18000000 INFO @ Wed, 08 Dec 2021 21:25:10: 11000000 INFO @ Wed, 08 Dec 2021 21:25:11: 8000000 INFO @ Wed, 08 Dec 2021 21:25:14: 19000000 INFO @ Wed, 08 Dec 2021 21:25:16: 12000000 INFO @ Wed, 08 Dec 2021 21:25:16: 9000000 INFO @ Wed, 08 Dec 2021 21:25:20: 20000000 INFO @ Wed, 08 Dec 2021 21:25:21: 13000000 INFO @ Wed, 08 Dec 2021 21:25:22: 10000000 INFO @ Wed, 08 Dec 2021 21:25:25: 21000000 INFO @ Wed, 08 Dec 2021 21:25:26: 14000000 INFO @ Wed, 08 Dec 2021 21:25:28: 11000000 INFO @ Wed, 08 Dec 2021 21:25:31: 15000000 INFO @ Wed, 08 Dec 2021 21:25:31: 22000000 INFO @ Wed, 08 Dec 2021 21:25:33: 12000000 INFO @ Wed, 08 Dec 2021 21:25:36: 16000000 INFO @ Wed, 08 Dec 2021 21:25:37: 23000000 INFO @ Wed, 08 Dec 2021 21:25:39: 13000000 INFO @ Wed, 08 Dec 2021 21:25:41: 17000000 INFO @ Wed, 08 Dec 2021 21:25:43: 24000000 INFO @ Wed, 08 Dec 2021 21:25:45: 14000000 INFO @ Wed, 08 Dec 2021 21:25:46: 18000000 INFO @ Wed, 08 Dec 2021 21:25:49: 25000000 INFO @ Wed, 08 Dec 2021 21:25:51: 15000000 INFO @ Wed, 08 Dec 2021 21:25:51: 19000000 INFO @ Wed, 08 Dec 2021 21:25:57: 16000000 INFO @ Wed, 08 Dec 2021 21:25:57: 20000000 INFO @ Wed, 08 Dec 2021 21:25:59: 26000000 INFO @ Wed, 08 Dec 2021 21:26:03: 21000000 INFO @ Wed, 08 Dec 2021 21:26:03: 17000000 INFO @ Wed, 08 Dec 2021 21:26:06: 27000000 INFO @ Wed, 08 Dec 2021 21:26:08: 22000000 INFO @ Wed, 08 Dec 2021 21:26:09: 18000000 INFO @ Wed, 08 Dec 2021 21:26:12: 28000000 INFO @ Wed, 08 Dec 2021 21:26:13: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:26:13: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:26:13: #1 total tags in treatment: 13115590 INFO @ Wed, 08 Dec 2021 21:26:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:26:13: #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 21:26:13: #1 tags after filtering in treatment: 12251961 INFO @ Wed, 08 Dec 2021 21:26:13: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:26:13: #1 finished! INFO @ Wed, 08 Dec 2021 21:26:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:26:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:26:14: 23000000 INFO @ Wed, 08 Dec 2021 21:26:14: #2 number of paired peaks: 351 WARNING @ Wed, 08 Dec 2021 21:26:14: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 08 Dec 2021 21:26:14: start model_add_line... INFO @ Wed, 08 Dec 2021 21:26:14: start X-correlation... INFO @ Wed, 08 Dec 2021 21:26:14: end of X-cor INFO @ Wed, 08 Dec 2021 21:26:14: #2 finished! INFO @ Wed, 08 Dec 2021 21:26:14: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 21:26:14: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 21:26:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.05_model.r INFO @ Wed, 08 Dec 2021 21:26:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:26:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:26:15: 19000000 INFO @ Wed, 08 Dec 2021 21:26:20: 20000000 INFO @ Wed, 08 Dec 2021 21:26:20: 24000000 INFO @ Wed, 08 Dec 2021 21:26:26: 25000000 INFO @ Wed, 08 Dec 2021 21:26:26: 21000000 INFO @ Wed, 08 Dec 2021 21:26:31: 26000000 INFO @ Wed, 08 Dec 2021 21:26:32: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:26:36: 27000000 INFO @ Wed, 08 Dec 2021 21:26:38: 23000000 INFO @ Wed, 08 Dec 2021 21:26:42: 28000000 INFO @ Wed, 08 Dec 2021 21:26:43: 24000000 INFO @ Wed, 08 Dec 2021 21:26:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:26:48: 25000000 INFO @ Wed, 08 Dec 2021 21:26:49: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:26:49: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:26:49: #1 total tags in treatment: 13115590 INFO @ Wed, 08 Dec 2021 21:26:49: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:26:49: #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 21:26:49: #1 tags after filtering in treatment: 12251961 INFO @ Wed, 08 Dec 2021 21:26:49: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:26:49: #1 finished! INFO @ Wed, 08 Dec 2021 21:26:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:26:50: #2 number of paired peaks: 351 WARNING @ Wed, 08 Dec 2021 21:26:50: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 08 Dec 2021 21:26:50: start model_add_line... INFO @ Wed, 08 Dec 2021 21:26:50: start X-correlation... INFO @ Wed, 08 Dec 2021 21:26:50: end of X-cor INFO @ Wed, 08 Dec 2021 21:26:50: #2 finished! INFO @ Wed, 08 Dec 2021 21:26:50: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 21:26:50: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 21:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.10_model.r INFO @ Wed, 08 Dec 2021 21:26:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:26:53: 26000000 INFO @ Wed, 08 Dec 2021 21:26:58: 27000000 INFO @ Wed, 08 Dec 2021 21:27:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:27:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:27:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.05_summits.bed INFO @ Wed, 08 Dec 2021 21:27:03: Done! INFO @ Wed, 08 Dec 2021 21:27:03: 28000000 INFO @ Wed, 08 Dec 2021 21:27:04: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:27:04: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:27:04: #1 total tags in treatment: 13115590 INFO @ Wed, 08 Dec 2021 21:27:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:27:04: #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 21:27:04: #1 tags after filtering in treatment: 12251961 INFO @ Wed, 08 Dec 2021 21:27:04: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:27:04: #1 finished! INFO @ Wed, 08 Dec 2021 21:27:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:27:05: #2 number of paired peaks: 351 WARNING @ Wed, 08 Dec 2021 21:27:05: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Wed, 08 Dec 2021 21:27:05: start model_add_line... INFO @ Wed, 08 Dec 2021 21:27:05: start X-correlation... INFO @ Wed, 08 Dec 2021 21:27:05: end of X-cor INFO @ Wed, 08 Dec 2021 21:27:05: #2 finished! INFO @ Wed, 08 Dec 2021 21:27:05: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 21:27:05: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 21:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.20_model.r INFO @ Wed, 08 Dec 2021 21:27:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:27:05: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 570 millis pass2 - checking and writing primary data (336 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:27:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:27:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.10_summits.bed INFO @ Wed, 08 Dec 2021 21:27:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976734/SRX8976734.20_summits.bed INFO @ Wed, 08 Dec 2021 21:27:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 1 millis CompletedMACS2peakCalling