Job ID = 14159313 SRX = SRX8976725 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: 00:09:49 12998729 reads; of these: 12998729 (100.00%) were paired; of these: 306264 (2.36%) aligned concordantly 0 times 10996541 (84.60%) aligned concordantly exactly 1 time 1695924 (13.05%) aligned concordantly >1 times ---- 306264 pairs aligned concordantly 0 times; of these: 171397 (55.96%) aligned discordantly 1 time ---- 134867 pairs aligned 0 times concordantly or discordantly; of these: 269734 mates make up the pairs; of these: 119488 (44.30%) aligned 0 times 79699 (29.55%) aligned exactly 1 time 70547 (26.15%) aligned >1 times 99.54% overall alignment rate Time searching: 00:09:49 Overall time: 00:09:49 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 8 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] 347147 / 12824910 = 0.0271 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 21:07:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.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 21:07:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:07:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:07:49: 1000000 INFO @ Wed, 08 Dec 2021 21:07:53: 2000000 INFO @ Wed, 08 Dec 2021 21:07:57: 3000000 INFO @ Wed, 08 Dec 2021 21:08:01: 4000000 INFO @ Wed, 08 Dec 2021 21:08:06: 5000000 INFO @ Wed, 08 Dec 2021 21:08:10: 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 21:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.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 21:08:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:08:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:08:14: 7000000 INFO @ Wed, 08 Dec 2021 21:08:19: 8000000 INFO @ Wed, 08 Dec 2021 21:08:20: 1000000 INFO @ Wed, 08 Dec 2021 21:08:24: 9000000 INFO @ Wed, 08 Dec 2021 21:08:25: 2000000 INFO @ Wed, 08 Dec 2021 21:08:29: 10000000 INFO @ Wed, 08 Dec 2021 21:08:30: 3000000 INFO @ Wed, 08 Dec 2021 21:08:34: 11000000 INFO @ Wed, 08 Dec 2021 21:08:36: 4000000 INFO @ Wed, 08 Dec 2021 21:08:38: 12000000 INFO @ Wed, 08 Dec 2021 21:08:41: 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 21:08:43: 13000000 INFO @ Wed, 08 Dec 2021 21:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.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 21:08:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:08:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:08:47: 6000000 INFO @ Wed, 08 Dec 2021 21:08:48: 14000000 INFO @ Wed, 08 Dec 2021 21:08:49: 1000000 INFO @ Wed, 08 Dec 2021 21:08:53: 15000000 INFO @ Wed, 08 Dec 2021 21:08:53: 7000000 INFO @ Wed, 08 Dec 2021 21:08:54: 2000000 INFO @ Wed, 08 Dec 2021 21:08:58: 16000000 INFO @ Wed, 08 Dec 2021 21:08:58: 8000000 INFO @ Wed, 08 Dec 2021 21:08:59: 3000000 INFO @ Wed, 08 Dec 2021 21:09:02: 17000000 INFO @ Wed, 08 Dec 2021 21:09:04: 9000000 INFO @ Wed, 08 Dec 2021 21:09:04: 4000000 INFO @ Wed, 08 Dec 2021 21:09:07: 18000000 INFO @ Wed, 08 Dec 2021 21:09:09: 5000000 INFO @ Wed, 08 Dec 2021 21:09:10: 10000000 INFO @ Wed, 08 Dec 2021 21:09:12: 19000000 INFO @ Wed, 08 Dec 2021 21:09:14: 6000000 INFO @ Wed, 08 Dec 2021 21:09:16: 11000000 INFO @ Wed, 08 Dec 2021 21:09:17: 20000000 INFO @ Wed, 08 Dec 2021 21:09:19: 7000000 INFO @ Wed, 08 Dec 2021 21:09:21: 12000000 INFO @ Wed, 08 Dec 2021 21:09:22: 21000000 INFO @ Wed, 08 Dec 2021 21:09:24: 8000000 INFO @ Wed, 08 Dec 2021 21:09:27: 22000000 INFO @ Wed, 08 Dec 2021 21:09:27: 13000000 INFO @ Wed, 08 Dec 2021 21:09:29: 9000000 INFO @ Wed, 08 Dec 2021 21:09:31: 23000000 INFO @ Wed, 08 Dec 2021 21:09:32: 14000000 INFO @ Wed, 08 Dec 2021 21:09:34: 10000000 INFO @ Wed, 08 Dec 2021 21:09:36: 24000000 INFO @ Wed, 08 Dec 2021 21:09:38: 15000000 INFO @ Wed, 08 Dec 2021 21:09:39: 11000000 INFO @ Wed, 08 Dec 2021 21:09:41: 25000000 INFO @ Wed, 08 Dec 2021 21:09:42: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:09:42: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:09:42: #1 total tags in treatment: 12348030 INFO @ Wed, 08 Dec 2021 21:09:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:09:42: #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 21:09:42: #1 tags after filtering in treatment: 11561645 INFO @ Wed, 08 Dec 2021 21:09:42: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:09:42: #1 finished! INFO @ Wed, 08 Dec 2021 21:09:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:09:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:09:43: #2 number of paired peaks: 305 WARNING @ Wed, 08 Dec 2021 21:09:43: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Wed, 08 Dec 2021 21:09:43: start model_add_line... INFO @ Wed, 08 Dec 2021 21:09:43: start X-correlation... INFO @ Wed, 08 Dec 2021 21:09:43: end of X-cor INFO @ Wed, 08 Dec 2021 21:09:43: #2 finished! INFO @ Wed, 08 Dec 2021 21:09:43: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 21:09:43: #2 alternative fragment length(s) may be 4,137,157,182 bps INFO @ Wed, 08 Dec 2021 21:09:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.05_model.r INFO @ Wed, 08 Dec 2021 21:09:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:09:44: 16000000 INFO @ Wed, 08 Dec 2021 21:09:44: 12000000 INFO @ Wed, 08 Dec 2021 21:09:49: 13000000 INFO @ Wed, 08 Dec 2021 21:09:49: 17000000 INFO @ Wed, 08 Dec 2021 21:09:54: 14000000 INFO @ Wed, 08 Dec 2021 21:09:55: 18000000 INFO @ Wed, 08 Dec 2021 21:09:58: 15000000 INFO @ Wed, 08 Dec 2021 21:10:00: 19000000 INFO @ Wed, 08 Dec 2021 21:10:03: 16000000 INFO @ Wed, 08 Dec 2021 21:10:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:10:06: 20000000 INFO @ Wed, 08 Dec 2021 21:10:08: 17000000 INFO @ Wed, 08 Dec 2021 21:10:12: 21000000 INFO @ Wed, 08 Dec 2021 21:10:13: 18000000 INFO @ Wed, 08 Dec 2021 21:10:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:10:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:10:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.05_summits.bed INFO @ Wed, 08 Dec 2021 21:10:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:10:17: 22000000 INFO @ Wed, 08 Dec 2021 21:10:18: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:10:23: 23000000 INFO @ Wed, 08 Dec 2021 21:10:23: 20000000 INFO @ Wed, 08 Dec 2021 21:10:28: 21000000 INFO @ Wed, 08 Dec 2021 21:10:28: 24000000 INFO @ Wed, 08 Dec 2021 21:10:32: 22000000 INFO @ Wed, 08 Dec 2021 21:10:34: 25000000 INFO @ Wed, 08 Dec 2021 21:10:35: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:10:35: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:10:35: #1 total tags in treatment: 12348030 INFO @ Wed, 08 Dec 2021 21:10:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:10:35: #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 21:10:35: #1 tags after filtering in treatment: 11561645 INFO @ Wed, 08 Dec 2021 21:10:35: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:10:35: #1 finished! INFO @ Wed, 08 Dec 2021 21:10:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:10:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:10:36: #2 number of paired peaks: 305 WARNING @ Wed, 08 Dec 2021 21:10:36: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Wed, 08 Dec 2021 21:10:36: start model_add_line... INFO @ Wed, 08 Dec 2021 21:10:36: start X-correlation... INFO @ Wed, 08 Dec 2021 21:10:36: end of X-cor INFO @ Wed, 08 Dec 2021 21:10:36: #2 finished! INFO @ Wed, 08 Dec 2021 21:10:36: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 21:10:36: #2 alternative fragment length(s) may be 4,137,157,182 bps INFO @ Wed, 08 Dec 2021 21:10:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.10_model.r INFO @ Wed, 08 Dec 2021 21:10:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:10:37: 23000000 INFO @ Wed, 08 Dec 2021 21:10:42: 24000000 INFO @ Wed, 08 Dec 2021 21:10:46: 25000000 INFO @ Wed, 08 Dec 2021 21:10:47: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:10:47: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:10:47: #1 total tags in treatment: 12348030 INFO @ Wed, 08 Dec 2021 21:10:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:10:47: #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 21:10:47: #1 tags after filtering in treatment: 11561645 INFO @ Wed, 08 Dec 2021 21:10:47: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:10:47: #1 finished! INFO @ Wed, 08 Dec 2021 21:10:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:10:48: #2 number of paired peaks: 305 WARNING @ Wed, 08 Dec 2021 21:10:48: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Wed, 08 Dec 2021 21:10:48: start model_add_line... INFO @ Wed, 08 Dec 2021 21:10:48: start X-correlation... INFO @ Wed, 08 Dec 2021 21:10:48: end of X-cor INFO @ Wed, 08 Dec 2021 21:10:48: #2 finished! INFO @ Wed, 08 Dec 2021 21:10:48: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 21:10:48: #2 alternative fragment length(s) may be 4,137,157,182 bps INFO @ Wed, 08 Dec 2021 21:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.20_model.r INFO @ Wed, 08 Dec 2021 21:10:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:10:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:11:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:11:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:11:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.10_summits.bed INFO @ Wed, 08 Dec 2021 21:11:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:11:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:11:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:11:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:11:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976725/SRX8976725.20_summits.bed INFO @ Wed, 08 Dec 2021 21:11:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 5 millis CompletedMACS2peakCalling