Job ID = 14158148 SRX = SRX10342572 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13485264 spots for SRR13964600/SRR13964600.sra Written 13485264 spots for SRR13964600/SRR13964600.sra Read 13533307 spots for SRR13964601/SRR13964601.sra Written 13533307 spots for SRR13964601/SRR13964601.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158771 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:53:09 27018571 reads; of these: 27018571 (100.00%) were paired; of these: 4738966 (17.54%) aligned concordantly 0 times 10004743 (37.03%) aligned concordantly exactly 1 time 12274862 (45.43%) aligned concordantly >1 times ---- 4738966 pairs aligned concordantly 0 times; of these: 1042533 (22.00%) aligned discordantly 1 time ---- 3696433 pairs aligned 0 times concordantly or discordantly; of these: 7392866 mates make up the pairs; of these: 4065539 (54.99%) aligned 0 times 1785894 (24.16%) aligned exactly 1 time 1541433 (20.85%) aligned >1 times 92.48% overall alignment rate Time searching: 00:53:09 Overall time: 00:53:09 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] 5153143 / 22624269 = 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 15:38:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 15:38:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:38:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:38:08: 1000000 INFO @ Wed, 08 Dec 2021 15:38:13: 2000000 INFO @ Wed, 08 Dec 2021 15:38:18: 3000000 INFO @ Wed, 08 Dec 2021 15:38:23: 4000000 INFO @ Wed, 08 Dec 2021 15:38:27: 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 15:38:32: 6000000 INFO @ Wed, 08 Dec 2021 15:38:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 15:38:33: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:38:33: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:38:37: 7000000 INFO @ Wed, 08 Dec 2021 15:38:38: 1000000 INFO @ Wed, 08 Dec 2021 15:38:42: 8000000 INFO @ Wed, 08 Dec 2021 15:38:44: 2000000 INFO @ Wed, 08 Dec 2021 15:38:47: 9000000 INFO @ Wed, 08 Dec 2021 15:38:49: 3000000 INFO @ Wed, 08 Dec 2021 15:38:52: 10000000 INFO @ Wed, 08 Dec 2021 15:38:54: 4000000 INFO @ Wed, 08 Dec 2021 15:38:56: 11000000 INFO @ Wed, 08 Dec 2021 15:39:00: 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 15:39:01: 12000000 INFO @ Wed, 08 Dec 2021 15:39:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 15:39:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:39:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:39:05: 6000000 INFO @ Wed, 08 Dec 2021 15:39:06: 13000000 INFO @ Wed, 08 Dec 2021 15:39:08: 1000000 INFO @ Wed, 08 Dec 2021 15:39:10: 7000000 INFO @ Wed, 08 Dec 2021 15:39:11: 14000000 INFO @ Wed, 08 Dec 2021 15:39:14: 2000000 INFO @ Wed, 08 Dec 2021 15:39:16: 8000000 INFO @ Wed, 08 Dec 2021 15:39:16: 15000000 INFO @ Wed, 08 Dec 2021 15:39:19: 3000000 INFO @ Wed, 08 Dec 2021 15:39:21: 16000000 INFO @ Wed, 08 Dec 2021 15:39:21: 9000000 INFO @ Wed, 08 Dec 2021 15:39:24: 4000000 INFO @ Wed, 08 Dec 2021 15:39:26: 17000000 INFO @ Wed, 08 Dec 2021 15:39:27: 10000000 INFO @ Wed, 08 Dec 2021 15:39:30: 5000000 INFO @ Wed, 08 Dec 2021 15:39:30: 18000000 INFO @ Wed, 08 Dec 2021 15:39:32: 11000000 INFO @ Wed, 08 Dec 2021 15:39:35: 19000000 INFO @ Wed, 08 Dec 2021 15:39:35: 6000000 INFO @ Wed, 08 Dec 2021 15:39:38: 12000000 INFO @ Wed, 08 Dec 2021 15:39:40: 20000000 INFO @ Wed, 08 Dec 2021 15:39:41: 7000000 INFO @ Wed, 08 Dec 2021 15:39:43: 13000000 INFO @ Wed, 08 Dec 2021 15:39:45: 21000000 INFO @ Wed, 08 Dec 2021 15:39:46: 8000000 INFO @ Wed, 08 Dec 2021 15:39:49: 14000000 INFO @ Wed, 08 Dec 2021 15:39:50: 22000000 INFO @ Wed, 08 Dec 2021 15:39:52: 9000000 INFO @ Wed, 08 Dec 2021 15:39:54: 23000000 INFO @ Wed, 08 Dec 2021 15:39:54: 15000000 INFO @ Wed, 08 Dec 2021 15:39:57: 10000000 INFO @ Wed, 08 Dec 2021 15:39:59: 24000000 INFO @ Wed, 08 Dec 2021 15:40:00: 16000000 INFO @ Wed, 08 Dec 2021 15:40:02: 11000000 INFO @ Wed, 08 Dec 2021 15:40:04: 25000000 INFO @ Wed, 08 Dec 2021 15:40:05: 17000000 INFO @ Wed, 08 Dec 2021 15:40:08: 12000000 INFO @ Wed, 08 Dec 2021 15:40:09: 26000000 INFO @ Wed, 08 Dec 2021 15:40:10: 18000000 INFO @ Wed, 08 Dec 2021 15:40:13: 13000000 INFO @ Wed, 08 Dec 2021 15:40:14: 27000000 INFO @ Wed, 08 Dec 2021 15:40:16: 19000000 INFO @ Wed, 08 Dec 2021 15:40:19: 14000000 INFO @ Wed, 08 Dec 2021 15:40:19: 28000000 INFO @ Wed, 08 Dec 2021 15:40:21: 20000000 INFO @ Wed, 08 Dec 2021 15:40:24: 29000000 INFO @ Wed, 08 Dec 2021 15:40:24: 15000000 INFO @ Wed, 08 Dec 2021 15:40:26: 21000000 INFO @ Wed, 08 Dec 2021 15:40:29: 30000000 INFO @ Wed, 08 Dec 2021 15:40:29: 16000000 INFO @ Wed, 08 Dec 2021 15:40:31: 22000000 INFO @ Wed, 08 Dec 2021 15:40:34: 31000000 INFO @ Wed, 08 Dec 2021 15:40:34: 17000000 INFO @ Wed, 08 Dec 2021 15:40:36: 23000000 INFO @ Wed, 08 Dec 2021 15:40:39: 32000000 INFO @ Wed, 08 Dec 2021 15:40:40: 18000000 INFO @ Wed, 08 Dec 2021 15:40:42: 24000000 INFO @ Wed, 08 Dec 2021 15:40:44: 33000000 INFO @ Wed, 08 Dec 2021 15:40:45: 19000000 INFO @ Wed, 08 Dec 2021 15:40:47: 25000000 INFO @ Wed, 08 Dec 2021 15:40:49: 34000000 INFO @ Wed, 08 Dec 2021 15:40:50: 20000000 INFO @ Wed, 08 Dec 2021 15:40:52: 26000000 INFO @ Wed, 08 Dec 2021 15:40:55: 35000000 INFO @ Wed, 08 Dec 2021 15:40:55: 21000000 INFO @ Wed, 08 Dec 2021 15:40:57: 27000000 INFO @ Wed, 08 Dec 2021 15:41:00: 36000000 INFO @ Wed, 08 Dec 2021 15:41:00: 22000000 INFO @ Wed, 08 Dec 2021 15:41:03: 28000000 INFO @ Wed, 08 Dec 2021 15:41:05: 37000000 INFO @ Wed, 08 Dec 2021 15:41:06: 23000000 INFO @ Wed, 08 Dec 2021 15:41:08: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:41:09: 38000000 INFO @ Wed, 08 Dec 2021 15:41:11: 24000000 INFO @ Wed, 08 Dec 2021 15:41:13: 30000000 INFO @ Wed, 08 Dec 2021 15:41:14: 39000000 INFO @ Wed, 08 Dec 2021 15:41:16: 25000000 INFO @ Wed, 08 Dec 2021 15:41:17: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:41:17: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:41:17: #1 total tags in treatment: 17180323 INFO @ Wed, 08 Dec 2021 15:41:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:41:17: #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 15:41:17: #1 tags after filtering in treatment: 8071629 INFO @ Wed, 08 Dec 2021 15:41:17: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 08 Dec 2021 15:41:17: #1 finished! INFO @ Wed, 08 Dec 2021 15:41:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:41:18: #2 number of paired peaks: 2291 INFO @ Wed, 08 Dec 2021 15:41:18: start model_add_line... INFO @ Wed, 08 Dec 2021 15:41:18: start X-correlation... INFO @ Wed, 08 Dec 2021 15:41:18: end of X-cor INFO @ Wed, 08 Dec 2021 15:41:18: #2 finished! INFO @ Wed, 08 Dec 2021 15:41:18: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 15:41:18: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 15:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.05_model.r INFO @ Wed, 08 Dec 2021 15:41:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:41:18: 31000000 INFO @ Wed, 08 Dec 2021 15:41:21: 26000000 INFO @ Wed, 08 Dec 2021 15:41:24: 32000000 INFO @ Wed, 08 Dec 2021 15:41:26: 27000000 INFO @ Wed, 08 Dec 2021 15:41:29: 33000000 INFO @ Wed, 08 Dec 2021 15:41:32: 28000000 INFO @ Wed, 08 Dec 2021 15:41:34: 34000000 INFO @ Wed, 08 Dec 2021 15:41:37: 29000000 INFO @ Wed, 08 Dec 2021 15:41:39: 35000000 INFO @ Wed, 08 Dec 2021 15:41:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:41:42: 30000000 INFO @ Wed, 08 Dec 2021 15:41:45: 36000000 INFO @ Wed, 08 Dec 2021 15:41:47: 31000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:41:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:41:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:41:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.05_summits.bed INFO @ Wed, 08 Dec 2021 15:41:49: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4532 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:41:50: 37000000 INFO @ Wed, 08 Dec 2021 15:41:52: 32000000 INFO @ Wed, 08 Dec 2021 15:41:55: 38000000 INFO @ Wed, 08 Dec 2021 15:41:58: 33000000 INFO @ Wed, 08 Dec 2021 15:42:00: 39000000 INFO @ Wed, 08 Dec 2021 15:42:03: 34000000 INFO @ Wed, 08 Dec 2021 15:42:03: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:42:03: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:42:03: #1 total tags in treatment: 17180323 INFO @ Wed, 08 Dec 2021 15:42:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:42:03: #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 15:42:04: #1 tags after filtering in treatment: 8071629 INFO @ Wed, 08 Dec 2021 15:42:04: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 08 Dec 2021 15:42:04: #1 finished! INFO @ Wed, 08 Dec 2021 15:42:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:42:04: #2 number of paired peaks: 2291 INFO @ Wed, 08 Dec 2021 15:42:04: start model_add_line... INFO @ Wed, 08 Dec 2021 15:42:04: start X-correlation... INFO @ Wed, 08 Dec 2021 15:42:04: end of X-cor INFO @ Wed, 08 Dec 2021 15:42:04: #2 finished! INFO @ Wed, 08 Dec 2021 15:42:04: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 15:42:04: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 15:42:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.10_model.r INFO @ Wed, 08 Dec 2021 15:42:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:42:08: 35000000 INFO @ Wed, 08 Dec 2021 15:42:13: 36000000 INFO @ Wed, 08 Dec 2021 15:42:18: 37000000 INFO @ Wed, 08 Dec 2021 15:42:23: 38000000 INFO @ Wed, 08 Dec 2021 15:42:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:42:28: 39000000 INFO @ Wed, 08 Dec 2021 15:42:31: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:42:31: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:42:31: #1 total tags in treatment: 17180323 INFO @ Wed, 08 Dec 2021 15:42:31: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:42:31: #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 15:42:31: #1 tags after filtering in treatment: 8071629 INFO @ Wed, 08 Dec 2021 15:42:31: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 08 Dec 2021 15:42:31: #1 finished! INFO @ Wed, 08 Dec 2021 15:42:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:42:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:42:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:42:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:42:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.10_summits.bed INFO @ Wed, 08 Dec 2021 15:42:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2770 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:42:32: #2 number of paired peaks: 2291 INFO @ Wed, 08 Dec 2021 15:42:32: start model_add_line... INFO @ Wed, 08 Dec 2021 15:42:32: start X-correlation... INFO @ Wed, 08 Dec 2021 15:42:32: end of X-cor INFO @ Wed, 08 Dec 2021 15:42:32: #2 finished! INFO @ Wed, 08 Dec 2021 15:42:32: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 15:42:32: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 15:42:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.20_model.r INFO @ Wed, 08 Dec 2021 15:42:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:42:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:42:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342572/SRX10342572.20_summits.bed INFO @ Wed, 08 Dec 2021 15:43:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1548 records, 4 fields): 3 millis CompletedMACS2peakCalling