Job ID = 14160332 SRX = SRX9555455 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21504004 spots for SRR13111106/SRR13111106.sra Written 21504004 spots for SRR13111106/SRR13111106.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160468 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:16:17 21504004 reads; of these: 21504004 (100.00%) were paired; of these: 1867439 (8.68%) aligned concordantly 0 times 17035765 (79.22%) aligned concordantly exactly 1 time 2600800 (12.09%) aligned concordantly >1 times ---- 1867439 pairs aligned concordantly 0 times; of these: 640379 (34.29%) aligned discordantly 1 time ---- 1227060 pairs aligned 0 times concordantly or discordantly; of these: 2454120 mates make up the pairs; of these: 1858796 (75.74%) aligned 0 times 392769 (16.00%) aligned exactly 1 time 202555 (8.25%) aligned >1 times 95.68% overall alignment rate Time searching: 00:16:18 Overall time: 00:16:18 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] 1346726 / 20245896 = 0.0665 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 01:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.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 01:54:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:54:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:54:46: 1000000 INFO @ Thu, 09 Dec 2021 01:54:50: 2000000 INFO @ Thu, 09 Dec 2021 01:54:54: 3000000 INFO @ Thu, 09 Dec 2021 01:54:58: 4000000 INFO @ Thu, 09 Dec 2021 01:55:02: 5000000 INFO @ Thu, 09 Dec 2021 01:55:06: 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 01:55:11: 7000000 INFO @ Thu, 09 Dec 2021 01:55:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.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 01:55:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:55:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:55:15: 8000000 INFO @ Thu, 09 Dec 2021 01:55:17: 1000000 INFO @ Thu, 09 Dec 2021 01:55:19: 9000000 INFO @ Thu, 09 Dec 2021 01:55:22: 2000000 INFO @ Thu, 09 Dec 2021 01:55:24: 10000000 INFO @ Thu, 09 Dec 2021 01:55:27: 3000000 INFO @ Thu, 09 Dec 2021 01:55:28: 11000000 INFO @ Thu, 09 Dec 2021 01:55:32: 4000000 INFO @ Thu, 09 Dec 2021 01:55:32: 12000000 INFO @ Thu, 09 Dec 2021 01:55:37: 13000000 INFO @ Thu, 09 Dec 2021 01:55:37: 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 @ Thu, 09 Dec 2021 01:55:41: 14000000 INFO @ Thu, 09 Dec 2021 01:55:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.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 01:55:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:55:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:55:42: 6000000 INFO @ Thu, 09 Dec 2021 01:55:45: 15000000 INFO @ Thu, 09 Dec 2021 01:55:46: 1000000 INFO @ Thu, 09 Dec 2021 01:55:47: 7000000 INFO @ Thu, 09 Dec 2021 01:55:50: 16000000 INFO @ Thu, 09 Dec 2021 01:55:50: 2000000 INFO @ Thu, 09 Dec 2021 01:55:52: 8000000 INFO @ Thu, 09 Dec 2021 01:55:54: 17000000 INFO @ Thu, 09 Dec 2021 01:55:54: 3000000 INFO @ Thu, 09 Dec 2021 01:55:57: 9000000 INFO @ Thu, 09 Dec 2021 01:55:58: 18000000 INFO @ Thu, 09 Dec 2021 01:55:59: 4000000 INFO @ Thu, 09 Dec 2021 01:56:02: 10000000 INFO @ Thu, 09 Dec 2021 01:56:03: 19000000 INFO @ Thu, 09 Dec 2021 01:56:03: 5000000 INFO @ Thu, 09 Dec 2021 01:56:07: 20000000 INFO @ Thu, 09 Dec 2021 01:56:07: 11000000 INFO @ Thu, 09 Dec 2021 01:56:07: 6000000 INFO @ Thu, 09 Dec 2021 01:56:11: 21000000 INFO @ Thu, 09 Dec 2021 01:56:11: 7000000 INFO @ Thu, 09 Dec 2021 01:56:12: 12000000 INFO @ Thu, 09 Dec 2021 01:56:16: 22000000 INFO @ Thu, 09 Dec 2021 01:56:16: 8000000 INFO @ Thu, 09 Dec 2021 01:56:17: 13000000 INFO @ Thu, 09 Dec 2021 01:56:20: 23000000 INFO @ Thu, 09 Dec 2021 01:56:20: 9000000 INFO @ Thu, 09 Dec 2021 01:56:22: 14000000 INFO @ Thu, 09 Dec 2021 01:56:24: 24000000 INFO @ Thu, 09 Dec 2021 01:56:24: 10000000 INFO @ Thu, 09 Dec 2021 01:56:27: 15000000 INFO @ Thu, 09 Dec 2021 01:56:29: 25000000 INFO @ Thu, 09 Dec 2021 01:56:29: 11000000 INFO @ Thu, 09 Dec 2021 01:56:33: 16000000 INFO @ Thu, 09 Dec 2021 01:56:33: 26000000 INFO @ Thu, 09 Dec 2021 01:56:33: 12000000 INFO @ Thu, 09 Dec 2021 01:56:37: 27000000 INFO @ Thu, 09 Dec 2021 01:56:37: 13000000 INFO @ Thu, 09 Dec 2021 01:56:38: 17000000 INFO @ Thu, 09 Dec 2021 01:56:41: 14000000 INFO @ Thu, 09 Dec 2021 01:56:41: 28000000 INFO @ Thu, 09 Dec 2021 01:56:43: 18000000 INFO @ Thu, 09 Dec 2021 01:56:46: 15000000 INFO @ Thu, 09 Dec 2021 01:56:46: 29000000 INFO @ Thu, 09 Dec 2021 01:56:48: 19000000 INFO @ Thu, 09 Dec 2021 01:56:50: 16000000 INFO @ Thu, 09 Dec 2021 01:56:50: 30000000 INFO @ Thu, 09 Dec 2021 01:56:53: 20000000 INFO @ Thu, 09 Dec 2021 01:56:54: 17000000 INFO @ Thu, 09 Dec 2021 01:56:55: 31000000 INFO @ Thu, 09 Dec 2021 01:56:58: 21000000 INFO @ Thu, 09 Dec 2021 01:56:59: 18000000 INFO @ Thu, 09 Dec 2021 01:56:59: 32000000 INFO @ Thu, 09 Dec 2021 01:57:03: 22000000 INFO @ Thu, 09 Dec 2021 01:57:03: 19000000 INFO @ Thu, 09 Dec 2021 01:57:03: 33000000 INFO @ Thu, 09 Dec 2021 01:57:07: 20000000 INFO @ Thu, 09 Dec 2021 01:57:07: 34000000 INFO @ Thu, 09 Dec 2021 01:57:08: 23000000 INFO @ Thu, 09 Dec 2021 01:57:11: 21000000 INFO @ Thu, 09 Dec 2021 01:57:12: 35000000 INFO @ Thu, 09 Dec 2021 01:57:13: 24000000 INFO @ Thu, 09 Dec 2021 01:57:16: 22000000 INFO @ Thu, 09 Dec 2021 01:57:16: 36000000 INFO @ Thu, 09 Dec 2021 01:57:18: 25000000 INFO @ Thu, 09 Dec 2021 01:57:20: 23000000 INFO @ Thu, 09 Dec 2021 01:57:20: 37000000 INFO @ Thu, 09 Dec 2021 01:57:23: 26000000 INFO @ Thu, 09 Dec 2021 01:57:24: 24000000 INFO @ Thu, 09 Dec 2021 01:57:24: 38000000 INFO @ Thu, 09 Dec 2021 01:57:27: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:57:27: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:57:27: #1 total tags in treatment: 18312422 INFO @ Thu, 09 Dec 2021 01:57:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:57:27: #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 01:57:27: #1 tags after filtering in treatment: 16633856 INFO @ Thu, 09 Dec 2021 01:57:27: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 01:57:27: #1 finished! INFO @ Thu, 09 Dec 2021 01:57:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:57:28: 27000000 INFO @ Thu, 09 Dec 2021 01:57:28: #2 number of paired peaks: 303 WARNING @ Thu, 09 Dec 2021 01:57:28: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 09 Dec 2021 01:57:28: start model_add_line... INFO @ Thu, 09 Dec 2021 01:57:28: start X-correlation... INFO @ Thu, 09 Dec 2021 01:57:28: end of X-cor INFO @ Thu, 09 Dec 2021 01:57:28: #2 finished! INFO @ Thu, 09 Dec 2021 01:57:28: #2 predicted fragment length is 130 bps INFO @ Thu, 09 Dec 2021 01:57:28: #2 alternative fragment length(s) may be 3,130 bps INFO @ Thu, 09 Dec 2021 01:57:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.05_model.r INFO @ Thu, 09 Dec 2021 01:57:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:57:29: 25000000 INFO @ Thu, 09 Dec 2021 01:57:32: 28000000 INFO @ Thu, 09 Dec 2021 01:57:33: 26000000 INFO @ Thu, 09 Dec 2021 01:57:37: 27000000 INFO @ Thu, 09 Dec 2021 01:57:37: 29000000 INFO @ Thu, 09 Dec 2021 01:57:41: 28000000 INFO @ Thu, 09 Dec 2021 01:57:42: 30000000 INFO @ Thu, 09 Dec 2021 01:57:46: 29000000 INFO @ Thu, 09 Dec 2021 01:57:47: 31000000 INFO @ Thu, 09 Dec 2021 01:57:50: 30000000 INFO @ Thu, 09 Dec 2021 01:57:52: 32000000 INFO @ Thu, 09 Dec 2021 01:57:54: 31000000 INFO @ Thu, 09 Dec 2021 01:57:57: 33000000 INFO @ Thu, 09 Dec 2021 01:57:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:57:59: 32000000 INFO @ Thu, 09 Dec 2021 01:58:02: 34000000 INFO @ Thu, 09 Dec 2021 01:58:03: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:58:07: 34000000 INFO @ Thu, 09 Dec 2021 01:58:07: 35000000 INFO @ Thu, 09 Dec 2021 01:58:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:58:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:58:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.05_summits.bed INFO @ Thu, 09 Dec 2021 01:58:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:58:11: 35000000 INFO @ Thu, 09 Dec 2021 01:58:12: 36000000 INFO @ Thu, 09 Dec 2021 01:58:16: 36000000 INFO @ Thu, 09 Dec 2021 01:58:17: 37000000 INFO @ Thu, 09 Dec 2021 01:58:20: 37000000 INFO @ Thu, 09 Dec 2021 01:58:22: 38000000 INFO @ Thu, 09 Dec 2021 01:58:24: 38000000 INFO @ Thu, 09 Dec 2021 01:58:25: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:58:25: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:58:25: #1 total tags in treatment: 18312422 INFO @ Thu, 09 Dec 2021 01:58:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:58:25: #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 01:58:25: #1 tags after filtering in treatment: 16633856 INFO @ Thu, 09 Dec 2021 01:58:25: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 01:58:25: #1 finished! INFO @ Thu, 09 Dec 2021 01:58:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:58:26: #2 number of paired peaks: 303 WARNING @ Thu, 09 Dec 2021 01:58:26: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 09 Dec 2021 01:58:26: start model_add_line... INFO @ Thu, 09 Dec 2021 01:58:26: start X-correlation... INFO @ Thu, 09 Dec 2021 01:58:26: end of X-cor INFO @ Thu, 09 Dec 2021 01:58:26: #2 finished! INFO @ Thu, 09 Dec 2021 01:58:26: #2 predicted fragment length is 130 bps INFO @ Thu, 09 Dec 2021 01:58:26: #2 alternative fragment length(s) may be 3,130 bps INFO @ Thu, 09 Dec 2021 01:58:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.10_model.r INFO @ Thu, 09 Dec 2021 01:58:26: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:58:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:58:26: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:58:26: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:58:26: #1 total tags in treatment: 18312422 INFO @ Thu, 09 Dec 2021 01:58:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:58:26: #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 01:58:27: #1 tags after filtering in treatment: 16633856 INFO @ Thu, 09 Dec 2021 01:58:27: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 01:58:27: #1 finished! INFO @ Thu, 09 Dec 2021 01:58:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:58:28: #2 number of paired peaks: 303 WARNING @ Thu, 09 Dec 2021 01:58:28: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Thu, 09 Dec 2021 01:58:28: start model_add_line... INFO @ Thu, 09 Dec 2021 01:58:28: start X-correlation... INFO @ Thu, 09 Dec 2021 01:58:28: end of X-cor INFO @ Thu, 09 Dec 2021 01:58:28: #2 finished! INFO @ Thu, 09 Dec 2021 01:58:28: #2 predicted fragment length is 130 bps INFO @ Thu, 09 Dec 2021 01:58:28: #2 alternative fragment length(s) may be 3,130 bps INFO @ Thu, 09 Dec 2021 01:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.20_model.r INFO @ Thu, 09 Dec 2021 01:58:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:58:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:58:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:59:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:59:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:59:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.10_summits.bed INFO @ Thu, 09 Dec 2021 01:59:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 52 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:59:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:59:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:59:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555455/SRX9555455.20_summits.bed INFO @ Thu, 09 Dec 2021 01:59:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 1 millis CompletedMACS2peakCalling