Job ID = 14159207 SRX = SRX8976709 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: 00:10:17 11138175 reads; of these: 11138175 (100.00%) were paired; of these: 2436988 (21.88%) aligned concordantly 0 times 7035715 (63.17%) aligned concordantly exactly 1 time 1665472 (14.95%) aligned concordantly >1 times ---- 2436988 pairs aligned concordantly 0 times; of these: 1652320 (67.80%) aligned discordantly 1 time ---- 784668 pairs aligned 0 times concordantly or discordantly; of these: 1569336 mates make up the pairs; of these: 571175 (36.40%) aligned 0 times 435857 (27.77%) aligned exactly 1 time 562304 (35.83%) aligned >1 times 97.44% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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] 409904 / 10347414 = 0.0396 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 20:27:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.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 20:27:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:27:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:27:47: 1000000 INFO @ Wed, 08 Dec 2021 20:27:52: 2000000 INFO @ Wed, 08 Dec 2021 20:27:57: 3000000 INFO @ Wed, 08 Dec 2021 20:28:02: 4000000 INFO @ Wed, 08 Dec 2021 20:28:07: 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 20:28:12: 6000000 INFO @ Wed, 08 Dec 2021 20:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.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 20:28:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:28:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:28:17: 1000000 INFO @ Wed, 08 Dec 2021 20:28:17: 7000000 INFO @ Wed, 08 Dec 2021 20:28:22: 2000000 INFO @ Wed, 08 Dec 2021 20:28:23: 8000000 INFO @ Wed, 08 Dec 2021 20:28:28: 9000000 INFO @ Wed, 08 Dec 2021 20:28:28: 3000000 INFO @ Wed, 08 Dec 2021 20:28:33: 10000000 INFO @ Wed, 08 Dec 2021 20:28:33: 4000000 INFO @ Wed, 08 Dec 2021 20:28:38: 11000000 INFO @ Wed, 08 Dec 2021 20:28:38: 5000000 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 20:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.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 20:28:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:28:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:28:43: 12000000 INFO @ Wed, 08 Dec 2021 20:28:43: 6000000 INFO @ Wed, 08 Dec 2021 20:28:47: 1000000 INFO @ Wed, 08 Dec 2021 20:28:48: 13000000 INFO @ Wed, 08 Dec 2021 20:28:48: 7000000 INFO @ Wed, 08 Dec 2021 20:28:52: 2000000 INFO @ Wed, 08 Dec 2021 20:28:53: 14000000 INFO @ Wed, 08 Dec 2021 20:28:53: 8000000 INFO @ Wed, 08 Dec 2021 20:28:57: 3000000 INFO @ Wed, 08 Dec 2021 20:28:58: 15000000 INFO @ Wed, 08 Dec 2021 20:28:59: 9000000 INFO @ Wed, 08 Dec 2021 20:29:02: 4000000 INFO @ Wed, 08 Dec 2021 20:29:03: 16000000 INFO @ Wed, 08 Dec 2021 20:29:04: 10000000 INFO @ Wed, 08 Dec 2021 20:29:07: 5000000 INFO @ Wed, 08 Dec 2021 20:29:08: 17000000 INFO @ Wed, 08 Dec 2021 20:29:08: 11000000 INFO @ Wed, 08 Dec 2021 20:29:11: 6000000 INFO @ Wed, 08 Dec 2021 20:29:12: 12000000 INFO @ Wed, 08 Dec 2021 20:29:13: 18000000 INFO @ Wed, 08 Dec 2021 20:29:16: 7000000 INFO @ Wed, 08 Dec 2021 20:29:17: 13000000 INFO @ Wed, 08 Dec 2021 20:29:18: 19000000 INFO @ Wed, 08 Dec 2021 20:29:21: 8000000 INFO @ Wed, 08 Dec 2021 20:29:22: 14000000 INFO @ Wed, 08 Dec 2021 20:29:23: 20000000 INFO @ Wed, 08 Dec 2021 20:29:26: 9000000 INFO @ Wed, 08 Dec 2021 20:29:27: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:29:27: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:29:27: #1 total tags in treatment: 8333107 INFO @ Wed, 08 Dec 2021 20:29:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:29:27: #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 20:29:27: #1 tags after filtering in treatment: 7624949 INFO @ Wed, 08 Dec 2021 20:29:27: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:29:27: #1 finished! INFO @ Wed, 08 Dec 2021 20:29:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:29:28: 15000000 INFO @ Wed, 08 Dec 2021 20:29:28: #2 number of paired peaks: 561 WARNING @ Wed, 08 Dec 2021 20:29:28: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Wed, 08 Dec 2021 20:29:28: start model_add_line... INFO @ Wed, 08 Dec 2021 20:29:28: start X-correlation... INFO @ Wed, 08 Dec 2021 20:29:28: end of X-cor INFO @ Wed, 08 Dec 2021 20:29:28: #2 finished! INFO @ Wed, 08 Dec 2021 20:29:28: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 20:29:28: #2 alternative fragment length(s) may be 4,157,166 bps INFO @ Wed, 08 Dec 2021 20:29:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.05_model.r INFO @ Wed, 08 Dec 2021 20:29:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:29:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:29:31: 10000000 INFO @ Wed, 08 Dec 2021 20:29:33: 16000000 INFO @ Wed, 08 Dec 2021 20:29:36: 11000000 INFO @ Wed, 08 Dec 2021 20:29:38: 17000000 INFO @ Wed, 08 Dec 2021 20:29:40: 12000000 INFO @ Wed, 08 Dec 2021 20:29:43: 18000000 INFO @ Wed, 08 Dec 2021 20:29:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:29:45: 13000000 INFO @ Wed, 08 Dec 2021 20:29:48: 19000000 INFO @ Wed, 08 Dec 2021 20:29:50: 14000000 INFO @ Wed, 08 Dec 2021 20:29:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:29:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:29:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.05_summits.bed INFO @ Wed, 08 Dec 2021 20:29:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:29:53: 20000000 INFO @ Wed, 08 Dec 2021 20:29:55: 15000000 INFO @ Wed, 08 Dec 2021 20:29:58: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:29:58: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:29:58: #1 total tags in treatment: 8333107 INFO @ Wed, 08 Dec 2021 20:29:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:29:58: #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 20:29:58: #1 tags after filtering in treatment: 7624949 INFO @ Wed, 08 Dec 2021 20:29:58: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:29:58: #1 finished! INFO @ Wed, 08 Dec 2021 20:29:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:29:58: #2 number of paired peaks: 561 WARNING @ Wed, 08 Dec 2021 20:29:58: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Wed, 08 Dec 2021 20:29:58: start model_add_line... INFO @ Wed, 08 Dec 2021 20:29:58: start X-correlation... INFO @ Wed, 08 Dec 2021 20:29:58: end of X-cor INFO @ Wed, 08 Dec 2021 20:29:58: #2 finished! INFO @ Wed, 08 Dec 2021 20:29:58: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 20:29:58: #2 alternative fragment length(s) may be 4,157,166 bps INFO @ Wed, 08 Dec 2021 20:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.10_model.r INFO @ Wed, 08 Dec 2021 20:29:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:30:00: 16000000 INFO @ Wed, 08 Dec 2021 20:30:04: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:30:09: 18000000 INFO @ Wed, 08 Dec 2021 20:30:13: 19000000 INFO @ Wed, 08 Dec 2021 20:30:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:30:18: 20000000 INFO @ Wed, 08 Dec 2021 20:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.10_summits.bed INFO @ Wed, 08 Dec 2021 20:30:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:30:22: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:30:22: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:30:22: #1 total tags in treatment: 8333107 INFO @ Wed, 08 Dec 2021 20:30:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:30:22: #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 20:30:22: #1 tags after filtering in treatment: 7624949 INFO @ Wed, 08 Dec 2021 20:30:22: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:30:22: #1 finished! INFO @ Wed, 08 Dec 2021 20:30:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:30:23: #2 number of paired peaks: 561 WARNING @ Wed, 08 Dec 2021 20:30:23: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Wed, 08 Dec 2021 20:30:23: start model_add_line... INFO @ Wed, 08 Dec 2021 20:30:23: start X-correlation... INFO @ Wed, 08 Dec 2021 20:30:23: end of X-cor INFO @ Wed, 08 Dec 2021 20:30:23: #2 finished! INFO @ Wed, 08 Dec 2021 20:30:23: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 20:30:23: #2 alternative fragment length(s) may be 4,157,166 bps INFO @ Wed, 08 Dec 2021 20:30:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.20_model.r INFO @ Wed, 08 Dec 2021 20:30:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:30:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:30:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:30:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976709/SRX8976709.20_summits.bed INFO @ Wed, 08 Dec 2021 20:30:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (223 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。