Job ID = 14159138 SRX = SRX8976700 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: 00:00:01 Multiseed full-index search: 00:11:21 13717587 reads; of these: 13717587 (100.00%) were paired; of these: 1125571 (8.21%) aligned concordantly 0 times 10916177 (79.58%) aligned concordantly exactly 1 time 1675839 (12.22%) aligned concordantly >1 times ---- 1125571 pairs aligned concordantly 0 times; of these: 814049 (72.32%) aligned discordantly 1 time ---- 311522 pairs aligned 0 times concordantly or discordantly; of these: 623044 mates make up the pairs; of these: 228840 (36.73%) aligned 0 times 182147 (29.24%) aligned exactly 1 time 212057 (34.04%) aligned >1 times 99.17% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 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] 235985 / 13392754 = 0.0176 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 20:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.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 20:05:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:05:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:05:35: 1000000 INFO @ Wed, 08 Dec 2021 20:05:41: 2000000 INFO @ Wed, 08 Dec 2021 20:05:46: 3000000 INFO @ Wed, 08 Dec 2021 20:05:51: 4000000 INFO @ Wed, 08 Dec 2021 20:05:56: 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 20:05:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.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 20:05:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:05:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:06:02: 6000000 INFO @ Wed, 08 Dec 2021 20:06:04: 1000000 INFO @ Wed, 08 Dec 2021 20:06:07: 7000000 INFO @ Wed, 08 Dec 2021 20:06:09: 2000000 INFO @ Wed, 08 Dec 2021 20:06:13: 8000000 INFO @ Wed, 08 Dec 2021 20:06:14: 3000000 INFO @ Wed, 08 Dec 2021 20:06:18: 9000000 INFO @ Wed, 08 Dec 2021 20:06:19: 4000000 INFO @ Wed, 08 Dec 2021 20:06:24: 10000000 INFO @ Wed, 08 Dec 2021 20:06:24: 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 20:06:29: 6000000 INFO @ Wed, 08 Dec 2021 20:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.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 20:06:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:06:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:06:30: 11000000 INFO @ Wed, 08 Dec 2021 20:06:34: 7000000 INFO @ Wed, 08 Dec 2021 20:06:35: 12000000 INFO @ Wed, 08 Dec 2021 20:06:35: 1000000 INFO @ Wed, 08 Dec 2021 20:06:39: 8000000 INFO @ Wed, 08 Dec 2021 20:06:41: 13000000 INFO @ Wed, 08 Dec 2021 20:06:41: 2000000 INFO @ Wed, 08 Dec 2021 20:06:44: 9000000 INFO @ Wed, 08 Dec 2021 20:06:46: 14000000 INFO @ Wed, 08 Dec 2021 20:06:47: 3000000 INFO @ Wed, 08 Dec 2021 20:06:49: 10000000 INFO @ Wed, 08 Dec 2021 20:06:52: 15000000 INFO @ Wed, 08 Dec 2021 20:06:53: 4000000 INFO @ Wed, 08 Dec 2021 20:06:54: 11000000 INFO @ Wed, 08 Dec 2021 20:06:57: 16000000 INFO @ Wed, 08 Dec 2021 20:06:59: 12000000 INFO @ Wed, 08 Dec 2021 20:06:59: 5000000 INFO @ Wed, 08 Dec 2021 20:07:03: 17000000 INFO @ Wed, 08 Dec 2021 20:07:04: 13000000 INFO @ Wed, 08 Dec 2021 20:07:05: 6000000 INFO @ Wed, 08 Dec 2021 20:07:08: 18000000 INFO @ Wed, 08 Dec 2021 20:07:09: 14000000 INFO @ Wed, 08 Dec 2021 20:07:10: 7000000 INFO @ Wed, 08 Dec 2021 20:07:14: 15000000 INFO @ Wed, 08 Dec 2021 20:07:14: 19000000 INFO @ Wed, 08 Dec 2021 20:07:16: 8000000 INFO @ Wed, 08 Dec 2021 20:07:18: 16000000 INFO @ Wed, 08 Dec 2021 20:07:19: 20000000 INFO @ Wed, 08 Dec 2021 20:07:22: 9000000 INFO @ Wed, 08 Dec 2021 20:07:23: 17000000 INFO @ Wed, 08 Dec 2021 20:07:25: 21000000 INFO @ Wed, 08 Dec 2021 20:07:28: 10000000 INFO @ Wed, 08 Dec 2021 20:07:28: 18000000 INFO @ Wed, 08 Dec 2021 20:07:30: 22000000 INFO @ Wed, 08 Dec 2021 20:07:33: 19000000 INFO @ Wed, 08 Dec 2021 20:07:34: 11000000 INFO @ Wed, 08 Dec 2021 20:07:36: 23000000 INFO @ Wed, 08 Dec 2021 20:07:38: 20000000 INFO @ Wed, 08 Dec 2021 20:07:40: 12000000 INFO @ Wed, 08 Dec 2021 20:07:42: 24000000 INFO @ Wed, 08 Dec 2021 20:07:43: 21000000 INFO @ Wed, 08 Dec 2021 20:07:46: 13000000 INFO @ Wed, 08 Dec 2021 20:07:48: 25000000 INFO @ Wed, 08 Dec 2021 20:07:48: 22000000 INFO @ Wed, 08 Dec 2021 20:07:52: 14000000 INFO @ Wed, 08 Dec 2021 20:07:53: 23000000 INFO @ Wed, 08 Dec 2021 20:07:54: 26000000 INFO @ Wed, 08 Dec 2021 20:07:58: 15000000 INFO @ Wed, 08 Dec 2021 20:07:58: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:07:58: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:07:58: #1 total tags in treatment: 12365383 INFO @ Wed, 08 Dec 2021 20:07:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:07:58: #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 20:07:58: #1 tags after filtering in treatment: 11527632 INFO @ Wed, 08 Dec 2021 20:07:58: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:07:58: #1 finished! INFO @ Wed, 08 Dec 2021 20:07:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:07:58: 24000000 INFO @ Wed, 08 Dec 2021 20:07:59: #2 number of paired peaks: 361 WARNING @ Wed, 08 Dec 2021 20:07:59: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Wed, 08 Dec 2021 20:07:59: start model_add_line... INFO @ Wed, 08 Dec 2021 20:07:59: start X-correlation... INFO @ Wed, 08 Dec 2021 20:07:59: end of X-cor INFO @ Wed, 08 Dec 2021 20:07:59: #2 finished! INFO @ Wed, 08 Dec 2021 20:07:59: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 20:07:59: #2 alternative fragment length(s) may be 4,161,166 bps INFO @ Wed, 08 Dec 2021 20:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.05_model.r INFO @ Wed, 08 Dec 2021 20:07:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:08:03: 25000000 INFO @ Wed, 08 Dec 2021 20:08:04: 16000000 INFO @ Wed, 08 Dec 2021 20:08:08: 26000000 INFO @ Wed, 08 Dec 2021 20:08:09: 17000000 INFO @ Wed, 08 Dec 2021 20:08:12: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:08:12: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:08:12: #1 total tags in treatment: 12365383 INFO @ Wed, 08 Dec 2021 20:08:12: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:08:12: #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 20:08:12: #1 tags after filtering in treatment: 11527632 INFO @ Wed, 08 Dec 2021 20:08:12: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:08:12: #1 finished! INFO @ Wed, 08 Dec 2021 20:08:12: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:08:13: #2 number of paired peaks: 361 WARNING @ Wed, 08 Dec 2021 20:08:13: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Wed, 08 Dec 2021 20:08:13: start model_add_line... INFO @ Wed, 08 Dec 2021 20:08:13: start X-correlation... INFO @ Wed, 08 Dec 2021 20:08:13: end of X-cor INFO @ Wed, 08 Dec 2021 20:08:13: #2 finished! INFO @ Wed, 08 Dec 2021 20:08:13: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 20:08:13: #2 alternative fragment length(s) may be 4,161,166 bps INFO @ Wed, 08 Dec 2021 20:08:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.10_model.r INFO @ Wed, 08 Dec 2021 20:08:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:08:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:08:15: 18000000 INFO @ Wed, 08 Dec 2021 20:08:21: 19000000 INFO @ Wed, 08 Dec 2021 20:08:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:08:26: 20000000 INFO @ Wed, 08 Dec 2021 20:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.05_summits.bed INFO @ Wed, 08 Dec 2021 20:08:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (357 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:08:32: 21000000 INFO @ Wed, 08 Dec 2021 20:08:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:08:38: 22000000 INFO @ Wed, 08 Dec 2021 20:08:43: 23000000 INFO @ Wed, 08 Dec 2021 20:08:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:08:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:08:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.10_summits.bed INFO @ Wed, 08 Dec 2021 20:08:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (275 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:08:49: 24000000 INFO @ Wed, 08 Dec 2021 20:08:55: 25000000 INFO @ Wed, 08 Dec 2021 20:09:00: 26000000 INFO @ Wed, 08 Dec 2021 20:09:04: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:09:04: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:09:04: #1 total tags in treatment: 12365383 INFO @ Wed, 08 Dec 2021 20:09:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:09:04: #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 20:09:04: #1 tags after filtering in treatment: 11527632 INFO @ Wed, 08 Dec 2021 20:09:04: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:09:04: #1 finished! INFO @ Wed, 08 Dec 2021 20:09:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:09:05: #2 number of paired peaks: 361 WARNING @ Wed, 08 Dec 2021 20:09:05: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Wed, 08 Dec 2021 20:09:05: start model_add_line... INFO @ Wed, 08 Dec 2021 20:09:05: start X-correlation... INFO @ Wed, 08 Dec 2021 20:09:05: end of X-cor INFO @ Wed, 08 Dec 2021 20:09:05: #2 finished! INFO @ Wed, 08 Dec 2021 20:09:05: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 20:09:05: #2 alternative fragment length(s) may be 4,161,166 bps INFO @ Wed, 08 Dec 2021 20:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.20_model.r INFO @ Wed, 08 Dec 2021 20:09:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:09:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:09:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:09:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976700/SRX8976700.20_summits.bed INFO @ Wed, 08 Dec 2021 20:09:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling