Job ID = 14160656 SRX = SRX8582578 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: 00:23:11 29962090 reads; of these: 29962090 (100.00%) were paired; of these: 4024124 (13.43%) aligned concordantly 0 times 22466427 (74.98%) aligned concordantly exactly 1 time 3471539 (11.59%) aligned concordantly >1 times ---- 4024124 pairs aligned concordantly 0 times; of these: 2110879 (52.46%) aligned discordantly 1 time ---- 1913245 pairs aligned 0 times concordantly or discordantly; of these: 3826490 mates make up the pairs; of these: 2397722 (62.66%) aligned 0 times 848667 (22.18%) aligned exactly 1 time 580101 (15.16%) aligned >1 times 96.00% overall alignment rate Time searching: 00:23:12 Overall time: 00:23:12 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 24 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] 7756894 / 28036876 = 0.2767 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 @ Thu, 09 Dec 2021 04:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.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 @ Thu, 09 Dec 2021 04:07:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:07:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:07:51: 1000000 INFO @ Thu, 09 Dec 2021 04:07:57: 2000000 INFO @ Thu, 09 Dec 2021 04:08:02: 3000000 INFO @ Thu, 09 Dec 2021 04:08:08: 4000000 INFO @ Thu, 09 Dec 2021 04:08:13: 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 @ Thu, 09 Dec 2021 04:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.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 @ Thu, 09 Dec 2021 04:08:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:08:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:08:19: 6000000 INFO @ Thu, 09 Dec 2021 04:08:21: 1000000 INFO @ Thu, 09 Dec 2021 04:08:25: 7000000 INFO @ Thu, 09 Dec 2021 04:08:27: 2000000 INFO @ Thu, 09 Dec 2021 04:08:31: 8000000 INFO @ Thu, 09 Dec 2021 04:08:33: 3000000 INFO @ Thu, 09 Dec 2021 04:08:37: 9000000 INFO @ Thu, 09 Dec 2021 04:08:39: 4000000 INFO @ Thu, 09 Dec 2021 04:08:43: 10000000 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 @ Thu, 09 Dec 2021 04:08:45: 5000000 INFO @ Thu, 09 Dec 2021 04:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.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 @ Thu, 09 Dec 2021 04:08:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:08:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:08:49: 11000000 INFO @ Thu, 09 Dec 2021 04:08:51: 6000000 INFO @ Thu, 09 Dec 2021 04:08:51: 1000000 INFO @ Thu, 09 Dec 2021 04:08:55: 12000000 INFO @ Thu, 09 Dec 2021 04:08:56: 2000000 INFO @ Thu, 09 Dec 2021 04:08:57: 7000000 INFO @ Thu, 09 Dec 2021 04:09:00: 13000000 INFO @ Thu, 09 Dec 2021 04:09:01: 3000000 INFO @ Thu, 09 Dec 2021 04:09:03: 8000000 INFO @ Thu, 09 Dec 2021 04:09:06: 14000000 INFO @ Thu, 09 Dec 2021 04:09:07: 4000000 INFO @ Thu, 09 Dec 2021 04:09:09: 9000000 INFO @ Thu, 09 Dec 2021 04:09:12: 5000000 INFO @ Thu, 09 Dec 2021 04:09:12: 15000000 INFO @ Thu, 09 Dec 2021 04:09:14: 10000000 INFO @ Thu, 09 Dec 2021 04:09:17: 6000000 INFO @ Thu, 09 Dec 2021 04:09:18: 16000000 INFO @ Thu, 09 Dec 2021 04:09:20: 11000000 INFO @ Thu, 09 Dec 2021 04:09:23: 7000000 INFO @ Thu, 09 Dec 2021 04:09:24: 17000000 INFO @ Thu, 09 Dec 2021 04:09:26: 12000000 INFO @ Thu, 09 Dec 2021 04:09:28: 8000000 INFO @ Thu, 09 Dec 2021 04:09:30: 18000000 INFO @ Thu, 09 Dec 2021 04:09:32: 13000000 INFO @ Thu, 09 Dec 2021 04:09:33: 9000000 INFO @ Thu, 09 Dec 2021 04:09:36: 19000000 INFO @ Thu, 09 Dec 2021 04:09:38: 14000000 INFO @ Thu, 09 Dec 2021 04:09:38: 10000000 INFO @ Thu, 09 Dec 2021 04:09:42: 20000000 INFO @ Thu, 09 Dec 2021 04:09:44: 11000000 INFO @ Thu, 09 Dec 2021 04:09:44: 15000000 INFO @ Thu, 09 Dec 2021 04:09:48: 21000000 INFO @ Thu, 09 Dec 2021 04:09:49: 12000000 INFO @ Thu, 09 Dec 2021 04:09:50: 16000000 INFO @ Thu, 09 Dec 2021 04:09:54: 22000000 INFO @ Thu, 09 Dec 2021 04:09:54: 13000000 INFO @ Thu, 09 Dec 2021 04:09:56: 17000000 INFO @ Thu, 09 Dec 2021 04:10:00: 14000000 INFO @ Thu, 09 Dec 2021 04:10:00: 23000000 INFO @ Thu, 09 Dec 2021 04:10:02: 18000000 INFO @ Thu, 09 Dec 2021 04:10:05: 15000000 INFO @ Thu, 09 Dec 2021 04:10:06: 24000000 INFO @ Thu, 09 Dec 2021 04:10:08: 19000000 INFO @ Thu, 09 Dec 2021 04:10:11: 16000000 INFO @ Thu, 09 Dec 2021 04:10:12: 25000000 INFO @ Thu, 09 Dec 2021 04:10:14: 20000000 INFO @ Thu, 09 Dec 2021 04:10:16: 17000000 INFO @ Thu, 09 Dec 2021 04:10:18: 26000000 INFO @ Thu, 09 Dec 2021 04:10:20: 21000000 INFO @ Thu, 09 Dec 2021 04:10:21: 18000000 INFO @ Thu, 09 Dec 2021 04:10:24: 27000000 INFO @ Thu, 09 Dec 2021 04:10:26: 22000000 INFO @ Thu, 09 Dec 2021 04:10:26: 19000000 INFO @ Thu, 09 Dec 2021 04:10:30: 28000000 INFO @ Thu, 09 Dec 2021 04:10:31: 23000000 INFO @ Thu, 09 Dec 2021 04:10:32: 20000000 INFO @ Thu, 09 Dec 2021 04:10:36: 29000000 INFO @ Thu, 09 Dec 2021 04:10:37: 21000000 INFO @ Thu, 09 Dec 2021 04:10:37: 24000000 INFO @ Thu, 09 Dec 2021 04:10:42: 30000000 INFO @ Thu, 09 Dec 2021 04:10:42: 22000000 INFO @ Thu, 09 Dec 2021 04:10:43: 25000000 INFO @ Thu, 09 Dec 2021 04:10:47: 23000000 INFO @ Thu, 09 Dec 2021 04:10:48: 31000000 INFO @ Thu, 09 Dec 2021 04:10:49: 26000000 INFO @ Thu, 09 Dec 2021 04:10:53: 24000000 INFO @ Thu, 09 Dec 2021 04:10:53: 32000000 INFO @ Thu, 09 Dec 2021 04:10:55: 27000000 INFO @ Thu, 09 Dec 2021 04:10:58: 25000000 INFO @ Thu, 09 Dec 2021 04:10:59: 33000000 INFO @ Thu, 09 Dec 2021 04:11:01: 28000000 INFO @ Thu, 09 Dec 2021 04:11:03: 26000000 INFO @ Thu, 09 Dec 2021 04:11:05: 34000000 INFO @ Thu, 09 Dec 2021 04:11:07: 29000000 INFO @ Thu, 09 Dec 2021 04:11:08: 27000000 INFO @ Thu, 09 Dec 2021 04:11:11: 35000000 INFO @ Thu, 09 Dec 2021 04:11:12: 30000000 INFO @ Thu, 09 Dec 2021 04:11:14: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:11:17: 36000000 INFO @ Thu, 09 Dec 2021 04:11:18: 31000000 INFO @ Thu, 09 Dec 2021 04:11:19: 29000000 INFO @ Thu, 09 Dec 2021 04:11:23: 37000000 INFO @ Thu, 09 Dec 2021 04:11:24: 32000000 INFO @ Thu, 09 Dec 2021 04:11:24: 30000000 INFO @ Thu, 09 Dec 2021 04:11:29: 38000000 INFO @ Thu, 09 Dec 2021 04:11:29: 31000000 INFO @ Thu, 09 Dec 2021 04:11:30: 33000000 INFO @ Thu, 09 Dec 2021 04:11:35: 32000000 INFO @ Thu, 09 Dec 2021 04:11:35: 39000000 INFO @ Thu, 09 Dec 2021 04:11:36: 34000000 INFO @ Thu, 09 Dec 2021 04:11:40: 33000000 INFO @ Thu, 09 Dec 2021 04:11:41: 40000000 INFO @ Thu, 09 Dec 2021 04:11:42: 35000000 INFO @ Thu, 09 Dec 2021 04:11:45: 34000000 INFO @ Thu, 09 Dec 2021 04:11:46: 41000000 INFO @ Thu, 09 Dec 2021 04:11:47: 36000000 INFO @ Thu, 09 Dec 2021 04:11:50: 35000000 INFO @ Thu, 09 Dec 2021 04:11:52: 42000000 INFO @ Thu, 09 Dec 2021 04:11:52: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:11:52: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:11:52: #1 total tags in treatment: 18568472 INFO @ Thu, 09 Dec 2021 04:11:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:11:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:11:53: #1 tags after filtering in treatment: 16209244 INFO @ Thu, 09 Dec 2021 04:11:53: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 04:11:53: #1 finished! INFO @ Thu, 09 Dec 2021 04:11:53: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:11:53: 37000000 INFO @ Thu, 09 Dec 2021 04:11:54: #2 number of paired peaks: 531 WARNING @ Thu, 09 Dec 2021 04:11:54: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Thu, 09 Dec 2021 04:11:54: start model_add_line... INFO @ Thu, 09 Dec 2021 04:11:54: start X-correlation... INFO @ Thu, 09 Dec 2021 04:11:54: end of X-cor INFO @ Thu, 09 Dec 2021 04:11:54: #2 finished! INFO @ Thu, 09 Dec 2021 04:11:54: #2 predicted fragment length is 211 bps INFO @ Thu, 09 Dec 2021 04:11:54: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 09 Dec 2021 04:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.05_model.r INFO @ Thu, 09 Dec 2021 04:11:54: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:11:56: 36000000 INFO @ Thu, 09 Dec 2021 04:11:59: 38000000 INFO @ Thu, 09 Dec 2021 04:12:01: 37000000 INFO @ Thu, 09 Dec 2021 04:12:05: 39000000 INFO @ Thu, 09 Dec 2021 04:12:06: 38000000 INFO @ Thu, 09 Dec 2021 04:12:11: 40000000 INFO @ Thu, 09 Dec 2021 04:12:11: 39000000 INFO @ Thu, 09 Dec 2021 04:12:16: 40000000 INFO @ Thu, 09 Dec 2021 04:12:16: 41000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:12:21: 41000000 INFO @ Thu, 09 Dec 2021 04:12:22: 42000000 INFO @ Thu, 09 Dec 2021 04:12:22: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:12:22: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:12:22: #1 total tags in treatment: 18568472 INFO @ Thu, 09 Dec 2021 04:12:22: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:12:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:12:23: #1 tags after filtering in treatment: 16209244 INFO @ Thu, 09 Dec 2021 04:12:23: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 04:12:23: #1 finished! INFO @ Thu, 09 Dec 2021 04:12:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:12:24: #2 number of paired peaks: 531 WARNING @ Thu, 09 Dec 2021 04:12:24: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Thu, 09 Dec 2021 04:12:24: start model_add_line... INFO @ Thu, 09 Dec 2021 04:12:24: start X-correlation... INFO @ Thu, 09 Dec 2021 04:12:24: end of X-cor INFO @ Thu, 09 Dec 2021 04:12:24: #2 finished! INFO @ Thu, 09 Dec 2021 04:12:24: #2 predicted fragment length is 211 bps INFO @ Thu, 09 Dec 2021 04:12:24: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 09 Dec 2021 04:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.10_model.r INFO @ Thu, 09 Dec 2021 04:12:24: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:12:26: 42000000 INFO @ Thu, 09 Dec 2021 04:12:27: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:12:27: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:12:27: #1 total tags in treatment: 18568472 INFO @ Thu, 09 Dec 2021 04:12:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:12:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:12:27: #1 tags after filtering in treatment: 16209244 INFO @ Thu, 09 Dec 2021 04:12:27: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 09 Dec 2021 04:12:27: #1 finished! INFO @ Thu, 09 Dec 2021 04:12:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:12:28: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:12:28: #2 number of paired peaks: 531 WARNING @ Thu, 09 Dec 2021 04:12:28: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Thu, 09 Dec 2021 04:12:28: start model_add_line... INFO @ Thu, 09 Dec 2021 04:12:28: start X-correlation... INFO @ Thu, 09 Dec 2021 04:12:28: end of X-cor INFO @ Thu, 09 Dec 2021 04:12:28: #2 finished! INFO @ Thu, 09 Dec 2021 04:12:28: #2 predicted fragment length is 211 bps INFO @ Thu, 09 Dec 2021 04:12:28: #2 alternative fragment length(s) may be 211 bps INFO @ Thu, 09 Dec 2021 04:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.20_model.r INFO @ Thu, 09 Dec 2021 04:12:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.05_summits.bed INFO @ Thu, 09 Dec 2021 04:12:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9270 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:12:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:13:00: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.10_summits.bed INFO @ Thu, 09 Dec 2021 04:13:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6353 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8582578/SRX8582578.20_summits.bed INFO @ Thu, 09 Dec 2021 04:13:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3530 records, 4 fields): 5 millis CompletedMACS2peakCalling