Job ID = 6497342 SRX = SRX1353667 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:59:41 prefetch.2.10.7: 1) Downloading 'SRR2722821'... 2020-06-25T21:59:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:02:12 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:02:12 prefetch.2.10.7: 1) 'SRR2722821' was downloaded successfully Read 15113259 spots for SRR2722821/SRR2722821.sra Written 15113259 spots for SRR2722821/SRR2722821.sra 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: 00:13:52 15113259 reads; of these: 15113259 (100.00%) were paired; of these: 909784 (6.02%) aligned concordantly 0 times 12097266 (80.04%) aligned concordantly exactly 1 time 2106209 (13.94%) aligned concordantly >1 times ---- 909784 pairs aligned concordantly 0 times; of these: 288656 (31.73%) aligned discordantly 1 time ---- 621128 pairs aligned 0 times concordantly or discordantly; of these: 1242256 mates make up the pairs; of these: 848208 (68.28%) aligned 0 times 251851 (20.27%) aligned exactly 1 time 142197 (11.45%) aligned >1 times 97.19% overall alignment rate Time searching: 00:13:52 Overall time: 00:13:52 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 12 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] 278172 / 14400219 = 0.0193 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.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 @ Fri, 26 Jun 2020 07:26:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:26:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:26:52: 1000000 INFO @ Fri, 26 Jun 2020 07:26:56: 2000000 INFO @ Fri, 26 Jun 2020 07:27:00: 3000000 INFO @ Fri, 26 Jun 2020 07:27:04: 4000000 INFO @ Fri, 26 Jun 2020 07:27:09: 5000000 INFO @ Fri, 26 Jun 2020 07:27:13: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:27:17: 7000000 INFO @ Fri, 26 Jun 2020 07:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.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 @ Fri, 26 Jun 2020 07:27:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:22: 8000000 INFO @ Fri, 26 Jun 2020 07:27:22: 1000000 INFO @ Fri, 26 Jun 2020 07:27:26: 9000000 INFO @ Fri, 26 Jun 2020 07:27:27: 2000000 INFO @ Fri, 26 Jun 2020 07:27:30: 10000000 INFO @ Fri, 26 Jun 2020 07:27:32: 3000000 INFO @ Fri, 26 Jun 2020 07:27:35: 11000000 INFO @ Fri, 26 Jun 2020 07:27:37: 4000000 INFO @ Fri, 26 Jun 2020 07:27:39: 12000000 INFO @ Fri, 26 Jun 2020 07:27:43: 5000000 INFO @ Fri, 26 Jun 2020 07:27:44: 13000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:27:48: 6000000 INFO @ Fri, 26 Jun 2020 07:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.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 @ Fri, 26 Jun 2020 07:27:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:48: 14000000 INFO @ Fri, 26 Jun 2020 07:27:52: 1000000 INFO @ Fri, 26 Jun 2020 07:27:53: 15000000 INFO @ Fri, 26 Jun 2020 07:27:53: 7000000 INFO @ Fri, 26 Jun 2020 07:27:57: 2000000 INFO @ Fri, 26 Jun 2020 07:27:57: 16000000 INFO @ Fri, 26 Jun 2020 07:27:58: 8000000 INFO @ Fri, 26 Jun 2020 07:28:01: 3000000 INFO @ Fri, 26 Jun 2020 07:28:01: 17000000 INFO @ Fri, 26 Jun 2020 07:28:03: 9000000 INFO @ Fri, 26 Jun 2020 07:28:06: 4000000 INFO @ Fri, 26 Jun 2020 07:28:06: 18000000 INFO @ Fri, 26 Jun 2020 07:28:08: 10000000 INFO @ Fri, 26 Jun 2020 07:28:10: 5000000 INFO @ Fri, 26 Jun 2020 07:28:10: 19000000 INFO @ Fri, 26 Jun 2020 07:28:13: 11000000 INFO @ Fri, 26 Jun 2020 07:28:15: 6000000 INFO @ Fri, 26 Jun 2020 07:28:15: 20000000 INFO @ Fri, 26 Jun 2020 07:28:18: 12000000 INFO @ Fri, 26 Jun 2020 07:28:19: 7000000 INFO @ Fri, 26 Jun 2020 07:28:19: 21000000 INFO @ Fri, 26 Jun 2020 07:28:23: 13000000 INFO @ Fri, 26 Jun 2020 07:28:24: 8000000 INFO @ Fri, 26 Jun 2020 07:28:24: 22000000 INFO @ Fri, 26 Jun 2020 07:28:28: 14000000 INFO @ Fri, 26 Jun 2020 07:28:28: 9000000 INFO @ Fri, 26 Jun 2020 07:28:28: 23000000 INFO @ Fri, 26 Jun 2020 07:28:32: 15000000 INFO @ Fri, 26 Jun 2020 07:28:32: 10000000 INFO @ Fri, 26 Jun 2020 07:28:33: 24000000 INFO @ Fri, 26 Jun 2020 07:28:37: 11000000 INFO @ Fri, 26 Jun 2020 07:28:37: 25000000 INFO @ Fri, 26 Jun 2020 07:28:38: 16000000 INFO @ Fri, 26 Jun 2020 07:28:42: 12000000 INFO @ Fri, 26 Jun 2020 07:28:42: 26000000 INFO @ Fri, 26 Jun 2020 07:28:43: 17000000 INFO @ Fri, 26 Jun 2020 07:28:46: 13000000 INFO @ Fri, 26 Jun 2020 07:28:46: 27000000 INFO @ Fri, 26 Jun 2020 07:28:48: 18000000 INFO @ Fri, 26 Jun 2020 07:28:51: 14000000 INFO @ Fri, 26 Jun 2020 07:28:51: 28000000 INFO @ Fri, 26 Jun 2020 07:28:53: 19000000 INFO @ Fri, 26 Jun 2020 07:28:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:28:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:28:55: #1 total tags in treatment: 13926613 INFO @ Fri, 26 Jun 2020 07:28:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:28:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:28:55: #1 tags after filtering in treatment: 12919562 INFO @ Fri, 26 Jun 2020 07:28:55: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 07:28:55: #1 finished! INFO @ Fri, 26 Jun 2020 07:28:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:28:55: 15000000 INFO @ Fri, 26 Jun 2020 07:28:56: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 07:28:56: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 07:28:56: start model_add_line... INFO @ Fri, 26 Jun 2020 07:28:56: start X-correlation... INFO @ Fri, 26 Jun 2020 07:28:56: end of X-cor INFO @ Fri, 26 Jun 2020 07:28:56: #2 finished! INFO @ Fri, 26 Jun 2020 07:28:56: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 07:28:56: #2 alternative fragment length(s) may be 4,113,125 bps INFO @ Fri, 26 Jun 2020 07:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.05_model.r INFO @ Fri, 26 Jun 2020 07:28:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:58: 20000000 INFO @ Fri, 26 Jun 2020 07:29:00: 16000000 INFO @ Fri, 26 Jun 2020 07:29:03: 21000000 INFO @ Fri, 26 Jun 2020 07:29:04: 17000000 INFO @ Fri, 26 Jun 2020 07:29:08: 22000000 INFO @ Fri, 26 Jun 2020 07:29:09: 18000000 INFO @ Fri, 26 Jun 2020 07:29:13: 19000000 INFO @ Fri, 26 Jun 2020 07:29:14: 23000000 INFO @ Fri, 26 Jun 2020 07:29:18: 20000000 INFO @ Fri, 26 Jun 2020 07:29:19: 24000000 INFO @ Fri, 26 Jun 2020 07:29:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:29:22: 21000000 INFO @ Fri, 26 Jun 2020 07:29:24: 25000000 INFO @ Fri, 26 Jun 2020 07:29:27: 22000000 INFO @ Fri, 26 Jun 2020 07:29:29: 26000000 INFO @ Fri, 26 Jun 2020 07:29:31: 23000000 INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.05_summits.bed INFO @ Fri, 26 Jun 2020 07:29:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:29:34: 27000000 INFO @ Fri, 26 Jun 2020 07:29:36: 24000000 INFO @ Fri, 26 Jun 2020 07:29:40: 28000000 INFO @ Fri, 26 Jun 2020 07:29:40: 25000000 INFO @ Fri, 26 Jun 2020 07:29:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:29:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:29:44: #1 total tags in treatment: 13926613 INFO @ Fri, 26 Jun 2020 07:29:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:29:44: #1 tags after filtering in treatment: 12919562 INFO @ Fri, 26 Jun 2020 07:29:44: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 07:29:44: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:45: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 07:29:45: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:45: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:45: 26000000 INFO @ Fri, 26 Jun 2020 07:29:45: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:45: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:45: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:45: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 07:29:45: #2 alternative fragment length(s) may be 4,113,125 bps INFO @ Fri, 26 Jun 2020 07:29:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.10_model.r INFO @ Fri, 26 Jun 2020 07:29:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:29:50: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:29:54: 28000000 INFO @ Fri, 26 Jun 2020 07:29:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:29:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:29:58: #1 total tags in treatment: 13926613 INFO @ Fri, 26 Jun 2020 07:29:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:29:58: #1 tags after filtering in treatment: 12919562 INFO @ Fri, 26 Jun 2020 07:29:58: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 07:29:58: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:59: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 07:29:59: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:59: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:59: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:59: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:59: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:59: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 07:29:59: #2 alternative fragment length(s) may be 4,113,125 bps INFO @ Fri, 26 Jun 2020 07:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.20_model.r INFO @ Fri, 26 Jun 2020 07:29:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:30:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.10_summits.bed INFO @ Fri, 26 Jun 2020 07:30:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:30:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353667/SRX1353667.20_summits.bed INFO @ Fri, 26 Jun 2020 07:30:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。