Job ID = 14158771 SRX = SRX10342572 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: 00:55:56 27018571 reads; of these: 27018571 (100.00%) were paired; of these: 4737415 (17.53%) aligned concordantly 0 times 10004885 (37.03%) aligned concordantly exactly 1 time 12276271 (45.44%) aligned concordantly >1 times ---- 4737415 pairs aligned concordantly 0 times; of these: 1042737 (22.01%) aligned discordantly 1 time ---- 3694678 pairs aligned 0 times concordantly or discordantly; of these: 7389356 mates make up the pairs; of these: 4062361 (54.98%) aligned 0 times 1786037 (24.17%) aligned exactly 1 time 1540958 (20.85%) aligned >1 times 92.48% overall alignment rate Time searching: 00:55:56 Overall time: 00:55:56 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] 5153979 / 22625928 = 0.2278 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 18:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.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 18:53:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:53:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:53:57: 1000000 INFO @ Wed, 08 Dec 2021 18:54:02: 2000000 INFO @ Wed, 08 Dec 2021 18:54:08: 3000000 INFO @ Wed, 08 Dec 2021 18:54:13: 4000000 INFO @ Wed, 08 Dec 2021 18:54:19: 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 18:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.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 18:54:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:54:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:54:24: 6000000 INFO @ Wed, 08 Dec 2021 18:54:26: 1000000 INFO @ Wed, 08 Dec 2021 18:54:30: 7000000 INFO @ Wed, 08 Dec 2021 18:54:31: 2000000 INFO @ Wed, 08 Dec 2021 18:54:35: 3000000 INFO @ Wed, 08 Dec 2021 18:54:36: 8000000 INFO @ Wed, 08 Dec 2021 18:54:40: 4000000 INFO @ Wed, 08 Dec 2021 18:54:41: 9000000 INFO @ Wed, 08 Dec 2021 18:54:45: 5000000 INFO @ Wed, 08 Dec 2021 18:54:47: 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 @ Wed, 08 Dec 2021 18:54:50: 6000000 INFO @ Wed, 08 Dec 2021 18:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.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 18:54:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:54:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:54:53: 11000000 INFO @ Wed, 08 Dec 2021 18:54:54: 7000000 INFO @ Wed, 08 Dec 2021 18:54:57: 1000000 INFO @ Wed, 08 Dec 2021 18:54:58: 12000000 INFO @ Wed, 08 Dec 2021 18:54:59: 8000000 INFO @ Wed, 08 Dec 2021 18:55:03: 2000000 INFO @ Wed, 08 Dec 2021 18:55:04: 13000000 INFO @ Wed, 08 Dec 2021 18:55:04: 9000000 INFO @ Wed, 08 Dec 2021 18:55:08: 3000000 INFO @ Wed, 08 Dec 2021 18:55:09: 10000000 INFO @ Wed, 08 Dec 2021 18:55:10: 14000000 INFO @ Wed, 08 Dec 2021 18:55:14: 11000000 INFO @ Wed, 08 Dec 2021 18:55:14: 4000000 INFO @ Wed, 08 Dec 2021 18:55:16: 15000000 INFO @ Wed, 08 Dec 2021 18:55:18: 12000000 INFO @ Wed, 08 Dec 2021 18:55:20: 5000000 INFO @ Wed, 08 Dec 2021 18:55:21: 16000000 INFO @ Wed, 08 Dec 2021 18:55:23: 13000000 INFO @ Wed, 08 Dec 2021 18:55:25: 6000000 INFO @ Wed, 08 Dec 2021 18:55:27: 17000000 INFO @ Wed, 08 Dec 2021 18:55:28: 14000000 INFO @ Wed, 08 Dec 2021 18:55:31: 7000000 INFO @ Wed, 08 Dec 2021 18:55:33: 18000000 INFO @ Wed, 08 Dec 2021 18:55:33: 15000000 INFO @ Wed, 08 Dec 2021 18:55:37: 8000000 INFO @ Wed, 08 Dec 2021 18:55:38: 16000000 INFO @ Wed, 08 Dec 2021 18:55:38: 19000000 INFO @ Wed, 08 Dec 2021 18:55:42: 9000000 INFO @ Wed, 08 Dec 2021 18:55:43: 17000000 INFO @ Wed, 08 Dec 2021 18:55:44: 20000000 INFO @ Wed, 08 Dec 2021 18:55:48: 18000000 INFO @ Wed, 08 Dec 2021 18:55:48: 10000000 INFO @ Wed, 08 Dec 2021 18:55:49: 21000000 INFO @ Wed, 08 Dec 2021 18:55:53: 19000000 INFO @ Wed, 08 Dec 2021 18:55:53: 11000000 INFO @ Wed, 08 Dec 2021 18:55:55: 22000000 INFO @ Wed, 08 Dec 2021 18:55:58: 20000000 INFO @ Wed, 08 Dec 2021 18:55:59: 12000000 INFO @ Wed, 08 Dec 2021 18:56:00: 23000000 INFO @ Wed, 08 Dec 2021 18:56:02: 21000000 INFO @ Wed, 08 Dec 2021 18:56:05: 13000000 INFO @ Wed, 08 Dec 2021 18:56:06: 24000000 INFO @ Wed, 08 Dec 2021 18:56:07: 22000000 INFO @ Wed, 08 Dec 2021 18:56:10: 14000000 INFO @ Wed, 08 Dec 2021 18:56:11: 25000000 INFO @ Wed, 08 Dec 2021 18:56:12: 23000000 INFO @ Wed, 08 Dec 2021 18:56:16: 15000000 INFO @ Wed, 08 Dec 2021 18:56:17: 26000000 INFO @ Wed, 08 Dec 2021 18:56:17: 24000000 INFO @ Wed, 08 Dec 2021 18:56:21: 16000000 INFO @ Wed, 08 Dec 2021 18:56:22: 25000000 INFO @ Wed, 08 Dec 2021 18:56:22: 27000000 INFO @ Wed, 08 Dec 2021 18:56:27: 26000000 INFO @ Wed, 08 Dec 2021 18:56:27: 17000000 INFO @ Wed, 08 Dec 2021 18:56:28: 28000000 INFO @ Wed, 08 Dec 2021 18:56:32: 27000000 INFO @ Wed, 08 Dec 2021 18:56:32: 18000000 INFO @ Wed, 08 Dec 2021 18:56:33: 29000000 INFO @ Wed, 08 Dec 2021 18:56:36: 28000000 INFO @ Wed, 08 Dec 2021 18:56:38: 19000000 INFO @ Wed, 08 Dec 2021 18:56:39: 30000000 INFO @ Wed, 08 Dec 2021 18:56:41: 29000000 INFO @ Wed, 08 Dec 2021 18:56:44: 20000000 INFO @ Wed, 08 Dec 2021 18:56:45: 31000000 INFO @ Wed, 08 Dec 2021 18:56:46: 30000000 INFO @ Wed, 08 Dec 2021 18:56:50: 21000000 INFO @ Wed, 08 Dec 2021 18:56:51: 32000000 INFO @ Wed, 08 Dec 2021 18:56:51: 31000000 INFO @ Wed, 08 Dec 2021 18:56:56: 32000000 INFO @ Wed, 08 Dec 2021 18:56:56: 22000000 INFO @ Wed, 08 Dec 2021 18:56:56: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:57:01: 33000000 INFO @ Wed, 08 Dec 2021 18:57:02: 23000000 INFO @ Wed, 08 Dec 2021 18:57:02: 34000000 INFO @ Wed, 08 Dec 2021 18:57:05: 34000000 INFO @ Wed, 08 Dec 2021 18:57:07: 24000000 INFO @ Wed, 08 Dec 2021 18:57:08: 35000000 INFO @ Wed, 08 Dec 2021 18:57:10: 35000000 INFO @ Wed, 08 Dec 2021 18:57:13: 25000000 INFO @ Wed, 08 Dec 2021 18:57:14: 36000000 INFO @ Wed, 08 Dec 2021 18:57:15: 36000000 INFO @ Wed, 08 Dec 2021 18:57:19: 26000000 INFO @ Wed, 08 Dec 2021 18:57:19: 37000000 INFO @ Wed, 08 Dec 2021 18:57:20: 37000000 INFO @ Wed, 08 Dec 2021 18:57:25: 27000000 INFO @ Wed, 08 Dec 2021 18:57:25: 38000000 INFO @ Wed, 08 Dec 2021 18:57:26: 38000000 INFO @ Wed, 08 Dec 2021 18:57:31: 39000000 INFO @ Wed, 08 Dec 2021 18:57:31: 28000000 INFO @ Wed, 08 Dec 2021 18:57:32: 39000000 INFO @ Wed, 08 Dec 2021 18:57:35: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:57:35: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:57:35: #1 total tags in treatment: 17181090 INFO @ Wed, 08 Dec 2021 18:57:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:57:35: #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 18:57:35: #1 tags after filtering in treatment: 8071823 INFO @ Wed, 08 Dec 2021 18:57:35: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 08 Dec 2021 18:57:35: #1 finished! INFO @ Wed, 08 Dec 2021 18:57:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:57:36: #2 number of paired peaks: 2295 INFO @ Wed, 08 Dec 2021 18:57:36: start model_add_line... INFO @ Wed, 08 Dec 2021 18:57:36: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:57:36: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:57:36: #1 total tags in treatment: 17181090 INFO @ Wed, 08 Dec 2021 18:57:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:57:36: #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 18:57:36: start X-correlation... INFO @ Wed, 08 Dec 2021 18:57:36: end of X-cor INFO @ Wed, 08 Dec 2021 18:57:36: #2 finished! INFO @ Wed, 08 Dec 2021 18:57:36: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 18:57:36: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 18:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.05_model.r INFO @ Wed, 08 Dec 2021 18:57:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:57:36: #1 tags after filtering in treatment: 8071823 INFO @ Wed, 08 Dec 2021 18:57:36: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 08 Dec 2021 18:57:36: #1 finished! INFO @ Wed, 08 Dec 2021 18:57:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:57:37: 29000000 INFO @ Wed, 08 Dec 2021 18:57:37: #2 number of paired peaks: 2295 INFO @ Wed, 08 Dec 2021 18:57:37: start model_add_line... INFO @ Wed, 08 Dec 2021 18:57:37: start X-correlation... INFO @ Wed, 08 Dec 2021 18:57:37: end of X-cor INFO @ Wed, 08 Dec 2021 18:57:37: #2 finished! INFO @ Wed, 08 Dec 2021 18:57:37: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 18:57:37: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 18:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.10_model.r INFO @ Wed, 08 Dec 2021 18:57:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:57:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:57:42: 30000000 INFO @ Wed, 08 Dec 2021 18:57:48: 31000000 INFO @ Wed, 08 Dec 2021 18:57:54: 32000000 INFO @ Wed, 08 Dec 2021 18:57:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:57:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:57:59: 33000000 INFO @ Wed, 08 Dec 2021 18:58:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:58:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:58:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.10_summits.bed INFO @ Wed, 08 Dec 2021 18:58:04: Done! INFO @ Wed, 08 Dec 2021 18:58:05: 34000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2772 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.05_summits.bed INFO @ Wed, 08 Dec 2021 18:58:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4535 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:58:10: 35000000 INFO @ Wed, 08 Dec 2021 18:58:15: 36000000 INFO @ Wed, 08 Dec 2021 18:58:21: 37000000 INFO @ Wed, 08 Dec 2021 18:58:26: 38000000 INFO @ Wed, 08 Dec 2021 18:58:31: 39000000 INFO @ Wed, 08 Dec 2021 18:58:35: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:58:35: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:58:35: #1 total tags in treatment: 17181090 INFO @ Wed, 08 Dec 2021 18:58:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:58:35: #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 18:58:35: #1 tags after filtering in treatment: 8071823 INFO @ Wed, 08 Dec 2021 18:58:35: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 08 Dec 2021 18:58:35: #1 finished! INFO @ Wed, 08 Dec 2021 18:58:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:58:36: #2 number of paired peaks: 2295 INFO @ Wed, 08 Dec 2021 18:58:36: start model_add_line... INFO @ Wed, 08 Dec 2021 18:58:36: start X-correlation... INFO @ Wed, 08 Dec 2021 18:58:36: end of X-cor INFO @ Wed, 08 Dec 2021 18:58:36: #2 finished! INFO @ Wed, 08 Dec 2021 18:58:36: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 18:58:36: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 18:58:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.20_model.r INFO @ Wed, 08 Dec 2021 18:58:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:58:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:58:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:59:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342572/SRX10342572.20_summits.bed INFO @ Wed, 08 Dec 2021 18:59:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1546 records, 4 fields): 2 millis CompletedMACS2peakCalling