Job ID = 14160331 SRX = SRX9555454 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24005034 spots for SRR13111105/SRR13111105.sra Written 24005034 spots for SRR13111105/SRR13111105.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160472 ("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: 00:17:41 24005034 reads; of these: 24005034 (100.00%) were paired; of these: 2628924 (10.95%) aligned concordantly 0 times 18272110 (76.12%) aligned concordantly exactly 1 time 3104000 (12.93%) aligned concordantly >1 times ---- 2628924 pairs aligned concordantly 0 times; of these: 577009 (21.95%) aligned discordantly 1 time ---- 2051915 pairs aligned 0 times concordantly or discordantly; of these: 4103830 mates make up the pairs; of these: 3706704 (90.32%) aligned 0 times 213562 (5.20%) aligned exactly 1 time 183564 (4.47%) aligned >1 times 92.28% overall alignment rate Time searching: 00:17:41 Overall time: 00:17:41 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] 2815760 / 21940909 = 0.1283 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 01:55:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.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 01:55:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:55:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:55:47: 1000000 INFO @ Thu, 09 Dec 2021 01:55:51: 2000000 INFO @ Thu, 09 Dec 2021 01:55:55: 3000000 INFO @ Thu, 09 Dec 2021 01:55:59: 4000000 INFO @ Thu, 09 Dec 2021 01:56:03: 5000000 INFO @ Thu, 09 Dec 2021 01:56:07: 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 01:56:12: 7000000 INFO @ Thu, 09 Dec 2021 01:56:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.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 01:56:12: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:56:12: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:56:16: 8000000 INFO @ Thu, 09 Dec 2021 01:56:17: 1000000 INFO @ Thu, 09 Dec 2021 01:56:20: 9000000 INFO @ Thu, 09 Dec 2021 01:56:22: 2000000 INFO @ Thu, 09 Dec 2021 01:56:25: 10000000 INFO @ Thu, 09 Dec 2021 01:56:28: 3000000 INFO @ Thu, 09 Dec 2021 01:56:29: 11000000 INFO @ Thu, 09 Dec 2021 01:56:33: 4000000 INFO @ Thu, 09 Dec 2021 01:56:34: 12000000 INFO @ Thu, 09 Dec 2021 01:56:38: 5000000 INFO @ Thu, 09 Dec 2021 01:56:38: 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 01:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.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 01:56:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:56:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:56:43: 6000000 INFO @ Thu, 09 Dec 2021 01:56:43: 14000000 INFO @ Thu, 09 Dec 2021 01:56:47: 15000000 INFO @ Thu, 09 Dec 2021 01:56:48: 7000000 INFO @ Thu, 09 Dec 2021 01:56:48: 1000000 INFO @ Thu, 09 Dec 2021 01:56:51: 16000000 INFO @ Thu, 09 Dec 2021 01:56:53: 8000000 INFO @ Thu, 09 Dec 2021 01:56:53: 2000000 INFO @ Thu, 09 Dec 2021 01:56:56: 17000000 INFO @ Thu, 09 Dec 2021 01:56:58: 9000000 INFO @ Thu, 09 Dec 2021 01:56:58: 3000000 INFO @ Thu, 09 Dec 2021 01:57:00: 18000000 INFO @ Thu, 09 Dec 2021 01:57:02: 10000000 INFO @ Thu, 09 Dec 2021 01:57:03: 4000000 INFO @ Thu, 09 Dec 2021 01:57:05: 19000000 INFO @ Thu, 09 Dec 2021 01:57:07: 11000000 INFO @ Thu, 09 Dec 2021 01:57:09: 5000000 INFO @ Thu, 09 Dec 2021 01:57:09: 20000000 INFO @ Thu, 09 Dec 2021 01:57:12: 12000000 INFO @ Thu, 09 Dec 2021 01:57:13: 21000000 INFO @ Thu, 09 Dec 2021 01:57:14: 6000000 INFO @ Thu, 09 Dec 2021 01:57:17: 13000000 INFO @ Thu, 09 Dec 2021 01:57:18: 22000000 INFO @ Thu, 09 Dec 2021 01:57:19: 7000000 INFO @ Thu, 09 Dec 2021 01:57:22: 23000000 INFO @ Thu, 09 Dec 2021 01:57:22: 14000000 INFO @ Thu, 09 Dec 2021 01:57:24: 8000000 INFO @ Thu, 09 Dec 2021 01:57:26: 24000000 INFO @ Thu, 09 Dec 2021 01:57:27: 15000000 INFO @ Thu, 09 Dec 2021 01:57:29: 9000000 INFO @ Thu, 09 Dec 2021 01:57:31: 25000000 INFO @ Thu, 09 Dec 2021 01:57:32: 16000000 INFO @ Thu, 09 Dec 2021 01:57:35: 10000000 INFO @ Thu, 09 Dec 2021 01:57:35: 26000000 INFO @ Thu, 09 Dec 2021 01:57:37: 17000000 INFO @ Thu, 09 Dec 2021 01:57:40: 27000000 INFO @ Thu, 09 Dec 2021 01:57:40: 11000000 INFO @ Thu, 09 Dec 2021 01:57:42: 18000000 INFO @ Thu, 09 Dec 2021 01:57:44: 28000000 INFO @ Thu, 09 Dec 2021 01:57:45: 12000000 INFO @ Thu, 09 Dec 2021 01:57:47: 19000000 INFO @ Thu, 09 Dec 2021 01:57:48: 29000000 INFO @ Thu, 09 Dec 2021 01:57:50: 13000000 INFO @ Thu, 09 Dec 2021 01:57:52: 20000000 INFO @ Thu, 09 Dec 2021 01:57:53: 30000000 INFO @ Thu, 09 Dec 2021 01:57:55: 14000000 INFO @ Thu, 09 Dec 2021 01:57:57: 31000000 INFO @ Thu, 09 Dec 2021 01:57:57: 21000000 INFO @ Thu, 09 Dec 2021 01:58:00: 15000000 INFO @ Thu, 09 Dec 2021 01:58:01: 32000000 INFO @ Thu, 09 Dec 2021 01:58:02: 22000000 INFO @ Thu, 09 Dec 2021 01:58:05: 16000000 INFO @ Thu, 09 Dec 2021 01:58:06: 33000000 INFO @ Thu, 09 Dec 2021 01:58:07: 23000000 INFO @ Thu, 09 Dec 2021 01:58:10: 17000000 INFO @ Thu, 09 Dec 2021 01:58:10: 34000000 INFO @ Thu, 09 Dec 2021 01:58:12: 24000000 INFO @ Thu, 09 Dec 2021 01:58:14: 35000000 INFO @ Thu, 09 Dec 2021 01:58:15: 18000000 INFO @ Thu, 09 Dec 2021 01:58:17: 25000000 INFO @ Thu, 09 Dec 2021 01:58:19: 36000000 INFO @ Thu, 09 Dec 2021 01:58:20: 19000000 INFO @ Thu, 09 Dec 2021 01:58:22: 26000000 INFO @ Thu, 09 Dec 2021 01:58:23: 37000000 INFO @ Thu, 09 Dec 2021 01:58:25: 20000000 INFO @ Thu, 09 Dec 2021 01:58:27: 27000000 INFO @ Thu, 09 Dec 2021 01:58:27: 38000000 INFO @ Thu, 09 Dec 2021 01:58:30: 21000000 INFO @ Thu, 09 Dec 2021 01:58:30: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:58:30: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:58:30: #1 total tags in treatment: 18574254 INFO @ Thu, 09 Dec 2021 01:58:30: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:58:30: #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 01:58:30: #1 tags after filtering in treatment: 17077104 INFO @ Thu, 09 Dec 2021 01:58:30: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:58:30: #1 finished! INFO @ Thu, 09 Dec 2021 01:58:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:58:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:58:31: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 01:58:31: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 01:58:31: start model_add_line... INFO @ Thu, 09 Dec 2021 01:58:32: start X-correlation... INFO @ Thu, 09 Dec 2021 01:58:32: end of X-cor INFO @ Thu, 09 Dec 2021 01:58:32: #2 finished! INFO @ Thu, 09 Dec 2021 01:58:32: #2 predicted fragment length is 116 bps INFO @ Thu, 09 Dec 2021 01:58:32: #2 alternative fragment length(s) may be 3,116 bps INFO @ Thu, 09 Dec 2021 01:58:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.05_model.r INFO @ Thu, 09 Dec 2021 01:58:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:58:32: 28000000 INFO @ Thu, 09 Dec 2021 01:58:35: 22000000 INFO @ Thu, 09 Dec 2021 01:58:37: 29000000 INFO @ Thu, 09 Dec 2021 01:58:40: 23000000 INFO @ Thu, 09 Dec 2021 01:58:42: 30000000 INFO @ Thu, 09 Dec 2021 01:58:45: 24000000 INFO @ Thu, 09 Dec 2021 01:58:47: 31000000 INFO @ Thu, 09 Dec 2021 01:58:50: 25000000 INFO @ Thu, 09 Dec 2021 01:58:52: 32000000 INFO @ Thu, 09 Dec 2021 01:58:54: 26000000 INFO @ Thu, 09 Dec 2021 01:58:57: 33000000 INFO @ Thu, 09 Dec 2021 01:59:00: 27000000 INFO @ Thu, 09 Dec 2021 01:59:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:59:02: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:59:05: 28000000 INFO @ Thu, 09 Dec 2021 01:59:06: 35000000 INFO @ Thu, 09 Dec 2021 01:59:10: 29000000 INFO @ Thu, 09 Dec 2021 01:59:11: 36000000 INFO @ Thu, 09 Dec 2021 01:59:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:59:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:59:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.05_summits.bed INFO @ Thu, 09 Dec 2021 01:59:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (472 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:59:15: 30000000 INFO @ Thu, 09 Dec 2021 01:59:16: 37000000 INFO @ Thu, 09 Dec 2021 01:59:20: 31000000 INFO @ Thu, 09 Dec 2021 01:59:21: 38000000 INFO @ Thu, 09 Dec 2021 01:59:24: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:59:24: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:59:24: #1 total tags in treatment: 18574254 INFO @ Thu, 09 Dec 2021 01:59:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:59:24: #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 01:59:25: 32000000 INFO @ Thu, 09 Dec 2021 01:59:25: #1 tags after filtering in treatment: 17077104 INFO @ Thu, 09 Dec 2021 01:59:25: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:59:25: #1 finished! INFO @ Thu, 09 Dec 2021 01:59:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:59:26: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 01:59:26: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 01:59:26: start model_add_line... INFO @ Thu, 09 Dec 2021 01:59:26: start X-correlation... INFO @ Thu, 09 Dec 2021 01:59:26: end of X-cor INFO @ Thu, 09 Dec 2021 01:59:26: #2 finished! INFO @ Thu, 09 Dec 2021 01:59:26: #2 predicted fragment length is 116 bps INFO @ Thu, 09 Dec 2021 01:59:26: #2 alternative fragment length(s) may be 3,116 bps INFO @ Thu, 09 Dec 2021 01:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.10_model.r INFO @ Thu, 09 Dec 2021 01:59:26: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:59:29: 33000000 INFO @ Thu, 09 Dec 2021 01:59:34: 34000000 INFO @ Thu, 09 Dec 2021 01:59:39: 35000000 INFO @ Thu, 09 Dec 2021 01:59:44: 36000000 INFO @ Thu, 09 Dec 2021 01:59:49: 37000000 INFO @ Thu, 09 Dec 2021 01:59:54: 38000000 INFO @ Thu, 09 Dec 2021 01:59:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:59:57: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:59:57: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:59:57: #1 total tags in treatment: 18574254 INFO @ Thu, 09 Dec 2021 01:59:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:59:57: #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 01:59:57: #1 tags after filtering in treatment: 17077104 INFO @ Thu, 09 Dec 2021 01:59:57: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:59:57: #1 finished! INFO @ Thu, 09 Dec 2021 01:59:57: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:59:58: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 01:59:58: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 01:59:58: start model_add_line... INFO @ Thu, 09 Dec 2021 01:59:58: start X-correlation... INFO @ Thu, 09 Dec 2021 01:59:59: end of X-cor INFO @ Thu, 09 Dec 2021 01:59:59: #2 finished! INFO @ Thu, 09 Dec 2021 01:59:59: #2 predicted fragment length is 116 bps INFO @ Thu, 09 Dec 2021 01:59:59: #2 alternative fragment length(s) may be 3,116 bps INFO @ Thu, 09 Dec 2021 01:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.20_model.r INFO @ Thu, 09 Dec 2021 01:59:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.10_summits.bed INFO @ Thu, 09 Dec 2021 02:00:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (336 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:00:28: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:00:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:00:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:00:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555454/SRX9555454.20_summits.bed INFO @ Thu, 09 Dec 2021 02:00:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (230 records, 4 fields): 2 millis CompletedMACS2peakCalling