Job ID = 14159141 SRX = SRX8976703 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: 00:10:20 12237385 reads; of these: 12237385 (100.00%) were paired; of these: 986926 (8.06%) aligned concordantly 0 times 9745678 (79.64%) aligned concordantly exactly 1 time 1504781 (12.30%) aligned concordantly >1 times ---- 986926 pairs aligned concordantly 0 times; of these: 694941 (70.41%) aligned discordantly 1 time ---- 291985 pairs aligned 0 times concordantly or discordantly; of these: 583970 mates make up the pairs; of these: 245489 (42.04%) aligned 0 times 156791 (26.85%) aligned exactly 1 time 181690 (31.11%) aligned >1 times 99.00% overall alignment rate Time searching: 00:10:20 Overall time: 00:10:20 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] 201738 / 11934905 = 0.0169 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 20:12:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.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 20:12:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:12:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:12:18: 1000000 INFO @ Wed, 08 Dec 2021 20:12:24: 2000000 INFO @ Wed, 08 Dec 2021 20:12:30: 3000000 INFO @ Wed, 08 Dec 2021 20:12:36: 4000000 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 20:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.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 20:12:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:12:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:12:43: 5000000 INFO @ Wed, 08 Dec 2021 20:12:46: 1000000 INFO @ Wed, 08 Dec 2021 20:12:50: 6000000 INFO @ Wed, 08 Dec 2021 20:12:53: 2000000 INFO @ Wed, 08 Dec 2021 20:12:56: 7000000 INFO @ Wed, 08 Dec 2021 20:12:59: 3000000 INFO @ Wed, 08 Dec 2021 20:13:03: 8000000 INFO @ Wed, 08 Dec 2021 20:13:06: 4000000 BedGraph に変換中... INFO @ Wed, 08 Dec 2021 20:13:10: 9000000 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 20:13:12: 5000000 INFO @ Wed, 08 Dec 2021 20:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.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 20:13:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:13:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:13:17: 10000000 INFO @ Wed, 08 Dec 2021 20:13:19: 6000000 INFO @ Wed, 08 Dec 2021 20:13:20: 1000000 INFO @ Wed, 08 Dec 2021 20:13:24: 11000000 INFO @ Wed, 08 Dec 2021 20:13:26: 7000000 INFO @ Wed, 08 Dec 2021 20:13:27: 2000000 INFO @ Wed, 08 Dec 2021 20:13:30: 12000000 INFO @ Wed, 08 Dec 2021 20:13:33: 8000000 INFO @ Wed, 08 Dec 2021 20:13:34: 3000000 INFO @ Wed, 08 Dec 2021 20:13:37: 13000000 INFO @ Wed, 08 Dec 2021 20:13:40: 9000000 INFO @ Wed, 08 Dec 2021 20:13:40: 4000000 INFO @ Wed, 08 Dec 2021 20:13:44: 14000000 INFO @ Wed, 08 Dec 2021 20:13:46: 10000000 INFO @ Wed, 08 Dec 2021 20:13:47: 5000000 INFO @ Wed, 08 Dec 2021 20:13:51: 15000000 INFO @ Wed, 08 Dec 2021 20:13:53: 6000000 INFO @ Wed, 08 Dec 2021 20:13:53: 11000000 INFO @ Wed, 08 Dec 2021 20:13:58: 16000000 INFO @ Wed, 08 Dec 2021 20:13:59: 7000000 INFO @ Wed, 08 Dec 2021 20:14:00: 12000000 INFO @ Wed, 08 Dec 2021 20:14:05: 17000000 INFO @ Wed, 08 Dec 2021 20:14:06: 8000000 INFO @ Wed, 08 Dec 2021 20:14:07: 13000000 INFO @ Wed, 08 Dec 2021 20:14:12: 18000000 INFO @ Wed, 08 Dec 2021 20:14:12: 9000000 INFO @ Wed, 08 Dec 2021 20:14:14: 14000000 INFO @ Wed, 08 Dec 2021 20:14:18: 10000000 INFO @ Wed, 08 Dec 2021 20:14:18: 19000000 INFO @ Wed, 08 Dec 2021 20:14:21: 15000000 INFO @ Wed, 08 Dec 2021 20:14:24: 11000000 INFO @ Wed, 08 Dec 2021 20:14:25: 20000000 INFO @ Wed, 08 Dec 2021 20:14:28: 16000000 INFO @ Wed, 08 Dec 2021 20:14:30: 12000000 INFO @ Wed, 08 Dec 2021 20:14:32: 21000000 INFO @ Wed, 08 Dec 2021 20:14:34: 17000000 INFO @ Wed, 08 Dec 2021 20:14:36: 13000000 INFO @ Wed, 08 Dec 2021 20:14:39: 22000000 INFO @ Wed, 08 Dec 2021 20:14:41: 18000000 INFO @ Wed, 08 Dec 2021 20:14:42: 14000000 INFO @ Wed, 08 Dec 2021 20:14:45: 23000000 BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 20:14:48: 19000000 INFO @ Wed, 08 Dec 2021 20:14:48: 15000000 INFO @ Wed, 08 Dec 2021 20:14:51: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:14:51: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:14:51: #1 total tags in treatment: 11056268 INFO @ Wed, 08 Dec 2021 20:14:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:14:51: #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 20:14:51: #1 tags after filtering in treatment: 10392783 INFO @ Wed, 08 Dec 2021 20:14:51: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:14:51: #1 finished! INFO @ Wed, 08 Dec 2021 20:14:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:14:52: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 20:14:52: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 20:14:52: start model_add_line... INFO @ Wed, 08 Dec 2021 20:14:52: start X-correlation... INFO @ Wed, 08 Dec 2021 20:14:52: end of X-cor INFO @ Wed, 08 Dec 2021 20:14:52: #2 finished! INFO @ Wed, 08 Dec 2021 20:14:52: #2 predicted fragment length is 162 bps INFO @ Wed, 08 Dec 2021 20:14:52: #2 alternative fragment length(s) may be 4,162 bps INFO @ Wed, 08 Dec 2021 20:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.05_model.r INFO @ Wed, 08 Dec 2021 20:14:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:14:54: 16000000 INFO @ Wed, 08 Dec 2021 20:14:55: 20000000 INFO @ Wed, 08 Dec 2021 20:15:00: 17000000 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:15:01: 21000000 INFO @ Wed, 08 Dec 2021 20:15:05: 18000000 INFO @ Wed, 08 Dec 2021 20:15:07: 22000000 INFO @ Wed, 08 Dec 2021 20:15:11: 19000000 INFO @ Wed, 08 Dec 2021 20:15:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:15:14: 23000000 INFO @ Wed, 08 Dec 2021 20:15:17: 20000000 INFO @ Wed, 08 Dec 2021 20:15:19: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:15:19: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:15:19: #1 total tags in treatment: 11056268 INFO @ Wed, 08 Dec 2021 20:15:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:15:19: #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 20:15:19: #1 tags after filtering in treatment: 10392783 INFO @ Wed, 08 Dec 2021 20:15:19: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:15:19: #1 finished! INFO @ Wed, 08 Dec 2021 20:15:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:15:20: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 20:15:20: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 20:15:20: start model_add_line... INFO @ Wed, 08 Dec 2021 20:15:20: start X-correlation... INFO @ Wed, 08 Dec 2021 20:15:20: end of X-cor INFO @ Wed, 08 Dec 2021 20:15:20: #2 finished! INFO @ Wed, 08 Dec 2021 20:15:20: #2 predicted fragment length is 162 bps INFO @ Wed, 08 Dec 2021 20:15:20: #2 alternative fragment length(s) may be 4,162 bps INFO @ Wed, 08 Dec 2021 20:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.10_model.r INFO @ Wed, 08 Dec 2021 20:15:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:15:22: 21000000 INFO @ Wed, 08 Dec 2021 20:15:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:15:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:15:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.05_summits.bed INFO @ Wed, 08 Dec 2021 20:15:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (359 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:15:27: 22000000 INFO @ Wed, 08 Dec 2021 20:15:32: 23000000 INFO @ Wed, 08 Dec 2021 20:15:36: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:15:36: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:15:36: #1 total tags in treatment: 11056268 INFO @ Wed, 08 Dec 2021 20:15:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:15:36: #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 20:15:36: #1 tags after filtering in treatment: 10392783 INFO @ Wed, 08 Dec 2021 20:15:36: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:15:36: #1 finished! INFO @ Wed, 08 Dec 2021 20:15:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:15:37: #2 number of paired peaks: 363 WARNING @ Wed, 08 Dec 2021 20:15:37: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Wed, 08 Dec 2021 20:15:37: start model_add_line... INFO @ Wed, 08 Dec 2021 20:15:37: start X-correlation... INFO @ Wed, 08 Dec 2021 20:15:37: end of X-cor INFO @ Wed, 08 Dec 2021 20:15:37: #2 finished! INFO @ Wed, 08 Dec 2021 20:15:37: #2 predicted fragment length is 162 bps INFO @ Wed, 08 Dec 2021 20:15:37: #2 alternative fragment length(s) may be 4,162 bps INFO @ Wed, 08 Dec 2021 20:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.20_model.r INFO @ Wed, 08 Dec 2021 20:15:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:15:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:15:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:15:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:15:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.10_summits.bed INFO @ Wed, 08 Dec 2021 20:15:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:15:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:16:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:16:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:16:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976703/SRX8976703.20_summits.bed INFO @ Wed, 08 Dec 2021 20:16:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (189 records, 4 fields): 2 millis CompletedMACS2peakCalling