Job ID = 14160329 SRX = SRX9555452 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20936115 spots for SRR13111103/SRR13111103.sra Written 20936115 spots for SRR13111103/SRR13111103.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160466 ("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: 00:16:35 20936115 reads; of these: 20936115 (100.00%) were paired; of these: 1658724 (7.92%) aligned concordantly 0 times 16579329 (79.19%) aligned concordantly exactly 1 time 2698062 (12.89%) aligned concordantly >1 times ---- 1658724 pairs aligned concordantly 0 times; of these: 864727 (52.13%) aligned discordantly 1 time ---- 793997 pairs aligned 0 times concordantly or discordantly; of these: 1587994 mates make up the pairs; of these: 874754 (55.09%) aligned 0 times 453983 (28.59%) aligned exactly 1 time 259257 (16.33%) aligned >1 times 97.91% overall alignment rate Time searching: 00:16:35 Overall time: 00:16:35 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 20 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] 1293698 / 20132118 = 0.0643 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 01:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.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 01:53:52: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:53:52: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:53:56: 1000000 INFO @ Thu, 09 Dec 2021 01:54:00: 2000000 INFO @ Thu, 09 Dec 2021 01:54:04: 3000000 INFO @ Thu, 09 Dec 2021 01:54:09: 4000000 INFO @ Thu, 09 Dec 2021 01:54:13: 5000000 INFO @ Thu, 09 Dec 2021 01:54:17: 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 @ Thu, 09 Dec 2021 01:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.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 01:54:21: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:54:21: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:54:22: 7000000 INFO @ Thu, 09 Dec 2021 01:54:26: 8000000 INFO @ Thu, 09 Dec 2021 01:54:27: 1000000 INFO @ Thu, 09 Dec 2021 01:54:31: 9000000 INFO @ Thu, 09 Dec 2021 01:54:32: 2000000 INFO @ Thu, 09 Dec 2021 01:54:35: 10000000 INFO @ Thu, 09 Dec 2021 01:54:38: 3000000 INFO @ Thu, 09 Dec 2021 01:54:40: 11000000 INFO @ Thu, 09 Dec 2021 01:54:43: 4000000 INFO @ Thu, 09 Dec 2021 01:54:44: 12000000 INFO @ Thu, 09 Dec 2021 01:54:48: 5000000 INFO @ Thu, 09 Dec 2021 01:54:49: 13000000 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 01:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.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 01:54:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:54:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:54:54: 6000000 INFO @ Thu, 09 Dec 2021 01:54:54: 14000000 INFO @ Thu, 09 Dec 2021 01:54:56: 1000000 INFO @ Thu, 09 Dec 2021 01:54:58: 15000000 INFO @ Thu, 09 Dec 2021 01:54:59: 7000000 INFO @ Thu, 09 Dec 2021 01:55:01: 2000000 INFO @ Thu, 09 Dec 2021 01:55:03: 16000000 INFO @ Thu, 09 Dec 2021 01:55:04: 8000000 INFO @ Thu, 09 Dec 2021 01:55:05: 3000000 INFO @ Thu, 09 Dec 2021 01:55:07: 17000000 INFO @ Thu, 09 Dec 2021 01:55:10: 9000000 INFO @ Thu, 09 Dec 2021 01:55:10: 4000000 INFO @ Thu, 09 Dec 2021 01:55:12: 18000000 INFO @ Thu, 09 Dec 2021 01:55:15: 5000000 INFO @ Thu, 09 Dec 2021 01:55:15: 10000000 INFO @ Thu, 09 Dec 2021 01:55:17: 19000000 INFO @ Thu, 09 Dec 2021 01:55:19: 6000000 INFO @ Thu, 09 Dec 2021 01:55:20: 11000000 INFO @ Thu, 09 Dec 2021 01:55:21: 20000000 INFO @ Thu, 09 Dec 2021 01:55:24: 7000000 INFO @ Thu, 09 Dec 2021 01:55:26: 12000000 INFO @ Thu, 09 Dec 2021 01:55:26: 21000000 INFO @ Thu, 09 Dec 2021 01:55:28: 8000000 INFO @ Thu, 09 Dec 2021 01:55:30: 22000000 INFO @ Thu, 09 Dec 2021 01:55:31: 13000000 INFO @ Thu, 09 Dec 2021 01:55:33: 9000000 INFO @ Thu, 09 Dec 2021 01:55:35: 23000000 INFO @ Thu, 09 Dec 2021 01:55:36: 14000000 INFO @ Thu, 09 Dec 2021 01:55:37: 10000000 INFO @ Thu, 09 Dec 2021 01:55:40: 24000000 INFO @ Thu, 09 Dec 2021 01:55:42: 15000000 INFO @ Thu, 09 Dec 2021 01:55:42: 11000000 INFO @ Thu, 09 Dec 2021 01:55:44: 25000000 INFO @ Thu, 09 Dec 2021 01:55:47: 12000000 INFO @ Thu, 09 Dec 2021 01:55:47: 16000000 INFO @ Thu, 09 Dec 2021 01:55:49: 26000000 INFO @ Thu, 09 Dec 2021 01:55:51: 13000000 INFO @ Thu, 09 Dec 2021 01:55:52: 17000000 INFO @ Thu, 09 Dec 2021 01:55:53: 27000000 INFO @ Thu, 09 Dec 2021 01:55:56: 14000000 INFO @ Thu, 09 Dec 2021 01:55:58: 28000000 INFO @ Thu, 09 Dec 2021 01:55:58: 18000000 INFO @ Thu, 09 Dec 2021 01:56:00: 15000000 INFO @ Thu, 09 Dec 2021 01:56:02: 29000000 INFO @ Thu, 09 Dec 2021 01:56:03: 19000000 INFO @ Thu, 09 Dec 2021 01:56:05: 16000000 INFO @ Thu, 09 Dec 2021 01:56:07: 30000000 INFO @ Thu, 09 Dec 2021 01:56:09: 20000000 INFO @ Thu, 09 Dec 2021 01:56:09: 17000000 INFO @ Thu, 09 Dec 2021 01:56:12: 31000000 INFO @ Thu, 09 Dec 2021 01:56:14: 21000000 INFO @ Thu, 09 Dec 2021 01:56:14: 18000000 INFO @ Thu, 09 Dec 2021 01:56:16: 32000000 INFO @ Thu, 09 Dec 2021 01:56:19: 19000000 INFO @ Thu, 09 Dec 2021 01:56:19: 22000000 INFO @ Thu, 09 Dec 2021 01:56:21: 33000000 INFO @ Thu, 09 Dec 2021 01:56:23: 20000000 INFO @ Thu, 09 Dec 2021 01:56:25: 23000000 INFO @ Thu, 09 Dec 2021 01:56:25: 34000000 INFO @ Thu, 09 Dec 2021 01:56:28: 21000000 INFO @ Thu, 09 Dec 2021 01:56:30: 35000000 INFO @ Thu, 09 Dec 2021 01:56:30: 24000000 INFO @ Thu, 09 Dec 2021 01:56:32: 22000000 INFO @ Thu, 09 Dec 2021 01:56:34: 36000000 INFO @ Thu, 09 Dec 2021 01:56:35: 25000000 INFO @ Thu, 09 Dec 2021 01:56:37: 23000000 INFO @ Thu, 09 Dec 2021 01:56:39: 37000000 INFO @ Thu, 09 Dec 2021 01:56:40: 26000000 INFO @ Thu, 09 Dec 2021 01:56:41: 24000000 INFO @ Thu, 09 Dec 2021 01:56:43: 38000000 INFO @ Thu, 09 Dec 2021 01:56:45: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:56:45: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:56:45: #1 total tags in treatment: 18012636 INFO @ Thu, 09 Dec 2021 01:56:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:56:45: #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 01:56:46: #1 tags after filtering in treatment: 16630281 INFO @ Thu, 09 Dec 2021 01:56:46: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:56:46: #1 finished! INFO @ Thu, 09 Dec 2021 01:56:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:56:46: 27000000 INFO @ Thu, 09 Dec 2021 01:56:46: 25000000 INFO @ Thu, 09 Dec 2021 01:56:47: #2 number of paired peaks: 291 WARNING @ Thu, 09 Dec 2021 01:56:47: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Thu, 09 Dec 2021 01:56:47: start model_add_line... INFO @ Thu, 09 Dec 2021 01:56:47: start X-correlation... INFO @ Thu, 09 Dec 2021 01:56:47: end of X-cor INFO @ Thu, 09 Dec 2021 01:56:47: #2 finished! INFO @ Thu, 09 Dec 2021 01:56:47: #2 predicted fragment length is 131 bps INFO @ Thu, 09 Dec 2021 01:56:47: #2 alternative fragment length(s) may be 3,102,131,146 bps INFO @ Thu, 09 Dec 2021 01:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.05_model.r INFO @ Thu, 09 Dec 2021 01:56:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:56:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:56:50: 26000000 INFO @ Thu, 09 Dec 2021 01:56:51: 28000000 INFO @ Thu, 09 Dec 2021 01:56:55: 27000000 INFO @ Thu, 09 Dec 2021 01:56:56: 29000000 INFO @ Thu, 09 Dec 2021 01:56:59: 28000000 INFO @ Thu, 09 Dec 2021 01:57:02: 30000000 INFO @ Thu, 09 Dec 2021 01:57:04: 29000000 INFO @ Thu, 09 Dec 2021 01:57:07: 31000000 INFO @ Thu, 09 Dec 2021 01:57:08: 30000000 INFO @ Thu, 09 Dec 2021 01:57:12: 32000000 INFO @ Thu, 09 Dec 2021 01:57:13: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:57:16: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:57:17: 32000000 INFO @ Thu, 09 Dec 2021 01:57:18: 33000000 INFO @ Thu, 09 Dec 2021 01:57:22: 33000000 INFO @ Thu, 09 Dec 2021 01:57:23: 34000000 INFO @ Thu, 09 Dec 2021 01:57:27: 34000000 INFO @ Thu, 09 Dec 2021 01:57:28: 35000000 INFO @ Thu, 09 Dec 2021 01:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.05_summits.bed INFO @ Thu, 09 Dec 2021 01:57:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (452 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:57:32: 35000000 INFO @ Thu, 09 Dec 2021 01:57:34: 36000000 INFO @ Thu, 09 Dec 2021 01:57:36: 36000000 INFO @ Thu, 09 Dec 2021 01:57:39: 37000000 INFO @ Thu, 09 Dec 2021 01:57:41: 37000000 INFO @ Thu, 09 Dec 2021 01:57:44: 38000000 INFO @ Thu, 09 Dec 2021 01:57:46: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:57:46: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:57:46: #1 total tags in treatment: 18012636 INFO @ Thu, 09 Dec 2021 01:57:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:57:46: #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 01:57:46: 38000000 INFO @ Thu, 09 Dec 2021 01:57:47: #1 tags after filtering in treatment: 16630281 INFO @ Thu, 09 Dec 2021 01:57:47: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:57:47: #1 finished! INFO @ Thu, 09 Dec 2021 01:57:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:57:48: #2 number of paired peaks: 291 WARNING @ Thu, 09 Dec 2021 01:57:48: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Thu, 09 Dec 2021 01:57:48: start model_add_line... INFO @ Thu, 09 Dec 2021 01:57:48: start X-correlation... INFO @ Thu, 09 Dec 2021 01:57:48: end of X-cor INFO @ Thu, 09 Dec 2021 01:57:48: #2 finished! INFO @ Thu, 09 Dec 2021 01:57:48: #2 predicted fragment length is 131 bps INFO @ Thu, 09 Dec 2021 01:57:48: #2 alternative fragment length(s) may be 3,102,131,146 bps INFO @ Thu, 09 Dec 2021 01:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.10_model.r INFO @ Thu, 09 Dec 2021 01:57:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:57:48: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:57:48: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:57:48: #1 total tags in treatment: 18012636 INFO @ Thu, 09 Dec 2021 01:57:48: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:57:48: #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 01:57:49: #1 tags after filtering in treatment: 16630281 INFO @ Thu, 09 Dec 2021 01:57:49: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:57:49: #1 finished! INFO @ Thu, 09 Dec 2021 01:57:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:57:50: #2 number of paired peaks: 291 WARNING @ Thu, 09 Dec 2021 01:57:50: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Thu, 09 Dec 2021 01:57:50: start model_add_line... INFO @ Thu, 09 Dec 2021 01:57:50: start X-correlation... INFO @ Thu, 09 Dec 2021 01:57:50: end of X-cor INFO @ Thu, 09 Dec 2021 01:57:50: #2 finished! INFO @ Thu, 09 Dec 2021 01:57:50: #2 predicted fragment length is 131 bps INFO @ Thu, 09 Dec 2021 01:57:50: #2 alternative fragment length(s) may be 3,102,131,146 bps INFO @ Thu, 09 Dec 2021 01:57:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.20_model.r INFO @ Thu, 09 Dec 2021 01:57:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:57:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:58:17: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:58:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.10_summits.bed INFO @ Thu, 09 Dec 2021 01:58:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:58:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:58:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555452/SRX9555452.20_summits.bed INFO @ Thu, 09 Dec 2021 01:58:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 2 millis CompletedMACS2peakCalling