Job ID = 14158169 SRX = SRX10342600 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: 00:14:41 20409694 reads; of these: 20409694 (100.00%) were paired; of these: 8335180 (40.84%) aligned concordantly 0 times 10429150 (51.10%) aligned concordantly exactly 1 time 1645364 (8.06%) aligned concordantly >1 times ---- 8335180 pairs aligned concordantly 0 times; of these: 5296428 (63.54%) aligned discordantly 1 time ---- 3038752 pairs aligned 0 times concordantly or discordantly; of these: 6077504 mates make up the pairs; of these: 4096478 (67.40%) aligned 0 times 791489 (13.02%) aligned exactly 1 time 1189537 (19.57%) aligned >1 times 89.96% overall alignment rate Time searching: 00:14:41 Overall time: 00:14:41 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] 4479456 / 17364118 = 0.2580 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 14:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.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 14:56:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:56:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:56:47: 1000000 INFO @ Wed, 08 Dec 2021 14:56:51: 2000000 INFO @ Wed, 08 Dec 2021 14:56:56: 3000000 INFO @ Wed, 08 Dec 2021 14:57:00: 4000000 INFO @ Wed, 08 Dec 2021 14:57:04: 5000000 INFO @ Wed, 08 Dec 2021 14:57:09: 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 14:57:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.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 14:57:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:57:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:57:13: 7000000 INFO @ Wed, 08 Dec 2021 14:57:17: 1000000 INFO @ Wed, 08 Dec 2021 14:57:18: 8000000 INFO @ Wed, 08 Dec 2021 14:57:22: 9000000 INFO @ Wed, 08 Dec 2021 14:57:23: 2000000 INFO @ Wed, 08 Dec 2021 14:57:27: 10000000 INFO @ Wed, 08 Dec 2021 14:57:28: 3000000 INFO @ Wed, 08 Dec 2021 14:57:32: 11000000 INFO @ Wed, 08 Dec 2021 14:57:33: 4000000 INFO @ Wed, 08 Dec 2021 14:57:36: 12000000 INFO @ Wed, 08 Dec 2021 14:57:38: 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 14:57:41: 13000000 INFO @ Wed, 08 Dec 2021 14:57:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.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 14:57:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:57:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:57:44: 6000000 INFO @ Wed, 08 Dec 2021 14:57:46: 14000000 INFO @ Wed, 08 Dec 2021 14:57:47: 1000000 INFO @ Wed, 08 Dec 2021 14:57:49: 7000000 INFO @ Wed, 08 Dec 2021 14:57:51: 15000000 INFO @ Wed, 08 Dec 2021 14:57:52: 2000000 INFO @ Wed, 08 Dec 2021 14:57:54: 8000000 INFO @ Wed, 08 Dec 2021 14:57:55: 16000000 INFO @ Wed, 08 Dec 2021 14:57:57: 3000000 INFO @ Wed, 08 Dec 2021 14:58:00: 9000000 INFO @ Wed, 08 Dec 2021 14:58:00: 17000000 INFO @ Wed, 08 Dec 2021 14:58:01: 4000000 INFO @ Wed, 08 Dec 2021 14:58:05: 10000000 INFO @ Wed, 08 Dec 2021 14:58:05: 18000000 INFO @ Wed, 08 Dec 2021 14:58:06: 5000000 INFO @ Wed, 08 Dec 2021 14:58:10: 19000000 INFO @ Wed, 08 Dec 2021 14:58:10: 11000000 INFO @ Wed, 08 Dec 2021 14:58:11: 6000000 INFO @ Wed, 08 Dec 2021 14:58:15: 20000000 INFO @ Wed, 08 Dec 2021 14:58:15: 12000000 INFO @ Wed, 08 Dec 2021 14:58:16: 7000000 INFO @ Wed, 08 Dec 2021 14:58:19: 21000000 INFO @ Wed, 08 Dec 2021 14:58:20: 8000000 INFO @ Wed, 08 Dec 2021 14:58:21: 13000000 INFO @ Wed, 08 Dec 2021 14:58:24: 22000000 INFO @ Wed, 08 Dec 2021 14:58:25: 9000000 INFO @ Wed, 08 Dec 2021 14:58:26: 14000000 INFO @ Wed, 08 Dec 2021 14:58:29: 23000000 INFO @ Wed, 08 Dec 2021 14:58:30: 10000000 INFO @ Wed, 08 Dec 2021 14:58:31: 15000000 INFO @ Wed, 08 Dec 2021 14:58:34: 24000000 INFO @ Wed, 08 Dec 2021 14:58:35: 11000000 INFO @ Wed, 08 Dec 2021 14:58:36: 16000000 INFO @ Wed, 08 Dec 2021 14:58:38: 25000000 INFO @ Wed, 08 Dec 2021 14:58:39: 12000000 INFO @ Wed, 08 Dec 2021 14:58:41: 17000000 INFO @ Wed, 08 Dec 2021 14:58:43: 26000000 INFO @ Wed, 08 Dec 2021 14:58:44: 13000000 INFO @ Wed, 08 Dec 2021 14:58:46: 18000000 INFO @ Wed, 08 Dec 2021 14:58:48: 27000000 INFO @ Wed, 08 Dec 2021 14:58:49: 14000000 INFO @ Wed, 08 Dec 2021 14:58:51: 19000000 INFO @ Wed, 08 Dec 2021 14:58:51: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 14:58:51: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 14:58:51: #1 total tags in treatment: 8697744 INFO @ Wed, 08 Dec 2021 14:58:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:58:51: #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 14:58:52: #1 tags after filtering in treatment: 8082490 INFO @ Wed, 08 Dec 2021 14:58:52: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 14:58:52: #1 finished! INFO @ Wed, 08 Dec 2021 14:58:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:58:52: #2 number of paired peaks: 543 WARNING @ Wed, 08 Dec 2021 14:58:52: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Wed, 08 Dec 2021 14:58:52: start model_add_line... INFO @ Wed, 08 Dec 2021 14:58:52: start X-correlation... INFO @ Wed, 08 Dec 2021 14:58:52: end of X-cor INFO @ Wed, 08 Dec 2021 14:58:52: #2 finished! INFO @ Wed, 08 Dec 2021 14:58:52: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 14:58:52: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 14:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.05_model.r INFO @ Wed, 08 Dec 2021 14:58:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:58:53: 15000000 INFO @ Wed, 08 Dec 2021 14:58:56: 20000000 INFO @ Wed, 08 Dec 2021 14:58:58: 16000000 INFO @ Wed, 08 Dec 2021 14:59:01: 21000000 INFO @ Wed, 08 Dec 2021 14:59:02: 17000000 INFO @ Wed, 08 Dec 2021 14:59:06: 22000000 INFO @ Wed, 08 Dec 2021 14:59:07: 18000000 INFO @ Wed, 08 Dec 2021 14:59:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:59:11: 23000000 INFO @ Wed, 08 Dec 2021 14:59:11: 19000000 INFO @ Wed, 08 Dec 2021 14:59:16: 20000000 INFO @ Wed, 08 Dec 2021 14:59:16: 24000000 INFO @ Wed, 08 Dec 2021 14:59:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:59:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:59:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.05_summits.bed INFO @ Wed, 08 Dec 2021 14:59:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1288 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:59:20: 21000000 INFO @ Wed, 08 Dec 2021 14:59:21: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:59:25: 22000000 INFO @ Wed, 08 Dec 2021 14:59:26: 26000000 INFO @ Wed, 08 Dec 2021 14:59:29: 23000000 INFO @ Wed, 08 Dec 2021 14:59:31: 27000000 INFO @ Wed, 08 Dec 2021 14:59:34: 24000000 INFO @ Wed, 08 Dec 2021 14:59:35: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 14:59:35: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 14:59:35: #1 total tags in treatment: 8697744 INFO @ Wed, 08 Dec 2021 14:59:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:59:35: #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 14:59:35: #1 tags after filtering in treatment: 8082490 INFO @ Wed, 08 Dec 2021 14:59:35: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 14:59:35: #1 finished! INFO @ Wed, 08 Dec 2021 14:59:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:59:36: #2 number of paired peaks: 543 WARNING @ Wed, 08 Dec 2021 14:59:36: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Wed, 08 Dec 2021 14:59:36: start model_add_line... INFO @ Wed, 08 Dec 2021 14:59:36: start X-correlation... INFO @ Wed, 08 Dec 2021 14:59:36: end of X-cor INFO @ Wed, 08 Dec 2021 14:59:36: #2 finished! INFO @ Wed, 08 Dec 2021 14:59:36: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 14:59:36: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 14:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.10_model.r INFO @ Wed, 08 Dec 2021 14:59:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:59:38: 25000000 INFO @ Wed, 08 Dec 2021 14:59:43: 26000000 INFO @ Wed, 08 Dec 2021 14:59:47: 27000000 INFO @ Wed, 08 Dec 2021 14:59:50: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 14:59:50: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 14:59:50: #1 total tags in treatment: 8697744 INFO @ Wed, 08 Dec 2021 14:59:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:59:50: #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 14:59:50: #1 tags after filtering in treatment: 8082490 INFO @ Wed, 08 Dec 2021 14:59:50: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 14:59:50: #1 finished! INFO @ Wed, 08 Dec 2021 14:59:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:59:51: #2 number of paired peaks: 543 WARNING @ Wed, 08 Dec 2021 14:59:51: Fewer paired peaks (543) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 543 pairs to build model! INFO @ Wed, 08 Dec 2021 14:59:51: start model_add_line... INFO @ Wed, 08 Dec 2021 14:59:51: start X-correlation... INFO @ Wed, 08 Dec 2021 14:59:51: end of X-cor INFO @ Wed, 08 Dec 2021 14:59:51: #2 finished! INFO @ Wed, 08 Dec 2021 14:59:51: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 14:59:51: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 14:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.20_model.r INFO @ Wed, 08 Dec 2021 14:59:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:59:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:00:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:00:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:00:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.10_summits.bed INFO @ Wed, 08 Dec 2021 15:00:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (433 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:00:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342600/SRX10342600.20_summits.bed INFO @ Wed, 08 Dec 2021 15:00:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 4 millis CompletedMACS2peakCalling