Job ID = 6507797 SRX = SRX4085428 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:41:46 prefetch.2.10.7: 1) Downloading 'SRR7167457'... 2020-06-26T13:41:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:47:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:47:23 prefetch.2.10.7: 1) 'SRR7167457' was downloaded successfully Read 22413526 spots for SRR7167457/SRR7167457.sra Written 22413526 spots for SRR7167457/SRR7167457.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: 00:20:43 22413526 reads; of these: 22413526 (100.00%) were paired; of these: 1269794 (5.67%) aligned concordantly 0 times 18365931 (81.94%) aligned concordantly exactly 1 time 2777801 (12.39%) aligned concordantly >1 times ---- 1269794 pairs aligned concordantly 0 times; of these: 616305 (48.54%) aligned discordantly 1 time ---- 653489 pairs aligned 0 times concordantly or discordantly; of these: 1306978 mates make up the pairs; of these: 531110 (40.64%) aligned 0 times 452381 (34.61%) aligned exactly 1 time 323487 (24.75%) aligned >1 times 98.82% overall alignment rate Time searching: 00:20:43 Overall time: 00:20:43 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] 8226342 / 21270460 = 0.3867 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 23:22:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.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 23:22:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:22:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:22:27: 1000000 INFO @ Fri, 26 Jun 2020 23:22:32: 2000000 INFO @ Fri, 26 Jun 2020 23:22:37: 3000000 INFO @ Fri, 26 Jun 2020 23:22:43: 4000000 INFO @ Fri, 26 Jun 2020 23:22:48: 5000000 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 23:22:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.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 23:22:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:22:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:22:53: 6000000 INFO @ Fri, 26 Jun 2020 23:22:57: 1000000 INFO @ Fri, 26 Jun 2020 23:22:59: 7000000 INFO @ Fri, 26 Jun 2020 23:23:02: 2000000 INFO @ Fri, 26 Jun 2020 23:23:05: 8000000 INFO @ Fri, 26 Jun 2020 23:23:08: 3000000 INFO @ Fri, 26 Jun 2020 23:23:10: 9000000 INFO @ Fri, 26 Jun 2020 23:23:14: 4000000 INFO @ Fri, 26 Jun 2020 23:23:16: 10000000 INFO @ Fri, 26 Jun 2020 23:23:19: 5000000 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 23:23:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.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 23:23:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:23:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:23:22: 11000000 INFO @ Fri, 26 Jun 2020 23:23:25: 6000000 INFO @ Fri, 26 Jun 2020 23:23:27: 12000000 INFO @ Fri, 26 Jun 2020 23:23:28: 1000000 INFO @ Fri, 26 Jun 2020 23:23:30: 7000000 INFO @ Fri, 26 Jun 2020 23:23:33: 13000000 INFO @ Fri, 26 Jun 2020 23:23:34: 2000000 INFO @ Fri, 26 Jun 2020 23:23:36: 8000000 INFO @ Fri, 26 Jun 2020 23:23:39: 14000000 INFO @ Fri, 26 Jun 2020 23:23:40: 3000000 INFO @ Fri, 26 Jun 2020 23:23:42: 9000000 INFO @ Fri, 26 Jun 2020 23:23:45: 15000000 INFO @ Fri, 26 Jun 2020 23:23:46: 4000000 INFO @ Fri, 26 Jun 2020 23:23:48: 10000000 INFO @ Fri, 26 Jun 2020 23:23:50: 16000000 INFO @ Fri, 26 Jun 2020 23:23:52: 5000000 INFO @ Fri, 26 Jun 2020 23:23:54: 11000000 INFO @ Fri, 26 Jun 2020 23:23:56: 17000000 INFO @ Fri, 26 Jun 2020 23:23:57: 6000000 INFO @ Fri, 26 Jun 2020 23:23:59: 12000000 INFO @ Fri, 26 Jun 2020 23:24:02: 18000000 INFO @ Fri, 26 Jun 2020 23:24:03: 7000000 INFO @ Fri, 26 Jun 2020 23:24:05: 13000000 INFO @ Fri, 26 Jun 2020 23:24:07: 19000000 INFO @ Fri, 26 Jun 2020 23:24:09: 8000000 INFO @ Fri, 26 Jun 2020 23:24:10: 14000000 INFO @ Fri, 26 Jun 2020 23:24:13: 20000000 INFO @ Fri, 26 Jun 2020 23:24:15: 9000000 INFO @ Fri, 26 Jun 2020 23:24:16: 15000000 INFO @ Fri, 26 Jun 2020 23:24:19: 21000000 INFO @ Fri, 26 Jun 2020 23:24:21: 16000000 INFO @ Fri, 26 Jun 2020 23:24:21: 10000000 INFO @ Fri, 26 Jun 2020 23:24:24: 22000000 INFO @ Fri, 26 Jun 2020 23:24:27: 17000000 INFO @ Fri, 26 Jun 2020 23:24:27: 11000000 INFO @ Fri, 26 Jun 2020 23:24:30: 23000000 INFO @ Fri, 26 Jun 2020 23:24:32: 18000000 INFO @ Fri, 26 Jun 2020 23:24:33: 12000000 INFO @ Fri, 26 Jun 2020 23:24:36: 24000000 INFO @ Fri, 26 Jun 2020 23:24:38: 19000000 INFO @ Fri, 26 Jun 2020 23:24:39: 13000000 INFO @ Fri, 26 Jun 2020 23:24:41: 25000000 INFO @ Fri, 26 Jun 2020 23:24:44: 20000000 INFO @ Fri, 26 Jun 2020 23:24:45: 14000000 INFO @ Fri, 26 Jun 2020 23:24:47: 26000000 INFO @ Fri, 26 Jun 2020 23:24:49: 21000000 INFO @ Fri, 26 Jun 2020 23:24:51: 15000000 INFO @ Fri, 26 Jun 2020 23:24:53: 27000000 INFO @ Fri, 26 Jun 2020 23:24:55: 22000000 INFO @ Fri, 26 Jun 2020 23:24:56: 16000000 INFO @ Fri, 26 Jun 2020 23:24:58: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:24:58: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:24:58: #1 total tags in treatment: 12961504 INFO @ Fri, 26 Jun 2020 23:24:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:24:58: #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 23:24:58: #1 tags after filtering in treatment: 10734218 INFO @ Fri, 26 Jun 2020 23:24:58: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 23:24:58: #1 finished! INFO @ Fri, 26 Jun 2020 23:24:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:24:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:24:59: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 23:24:59: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 23:24:59: start model_add_line... INFO @ Fri, 26 Jun 2020 23:24:59: start X-correlation... INFO @ Fri, 26 Jun 2020 23:24:59: end of X-cor INFO @ Fri, 26 Jun 2020 23:24:59: #2 finished! INFO @ Fri, 26 Jun 2020 23:24:59: #2 predicted fragment length is 127 bps INFO @ Fri, 26 Jun 2020 23:24:59: #2 alternative fragment length(s) may be 4,127 bps INFO @ Fri, 26 Jun 2020 23:24:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.05_model.r INFO @ Fri, 26 Jun 2020 23:24:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:24:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:25:00: 23000000 INFO @ Fri, 26 Jun 2020 23:25:02: 17000000 INFO @ Fri, 26 Jun 2020 23:25:06: 24000000 INFO @ Fri, 26 Jun 2020 23:25:08: 18000000 INFO @ Fri, 26 Jun 2020 23:25:12: 25000000 INFO @ Fri, 26 Jun 2020 23:25:14: 19000000 INFO @ Fri, 26 Jun 2020 23:25:18: 26000000 INFO @ Fri, 26 Jun 2020 23:25:20: 20000000 INFO @ Fri, 26 Jun 2020 23:25:23: 27000000 INFO @ Fri, 26 Jun 2020 23:25:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:25:26: 21000000 INFO @ Fri, 26 Jun 2020 23:25:28: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:25:28: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:25:28: #1 total tags in treatment: 12961504 INFO @ Fri, 26 Jun 2020 23:25:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:25:28: #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 23:25:28: #1 tags after filtering in treatment: 10734218 INFO @ Fri, 26 Jun 2020 23:25:28: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 23:25:28: #1 finished! INFO @ Fri, 26 Jun 2020 23:25:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:25:29: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 23:25:29: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 23:25:29: start model_add_line... INFO @ Fri, 26 Jun 2020 23:25:29: start X-correlation... INFO @ Fri, 26 Jun 2020 23:25:29: end of X-cor INFO @ Fri, 26 Jun 2020 23:25:29: #2 finished! INFO @ Fri, 26 Jun 2020 23:25:29: #2 predicted fragment length is 127 bps INFO @ Fri, 26 Jun 2020 23:25:29: #2 alternative fragment length(s) may be 4,127 bps INFO @ Fri, 26 Jun 2020 23:25:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.10_model.r INFO @ Fri, 26 Jun 2020 23:25:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:25:32: 22000000 INFO @ Fri, 26 Jun 2020 23:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.05_summits.bed INFO @ Fri, 26 Jun 2020 23:25:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1771 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:25:38: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:25:44: 24000000 INFO @ Fri, 26 Jun 2020 23:25:50: 25000000 INFO @ Fri, 26 Jun 2020 23:25:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:25:55: 26000000 INFO @ Fri, 26 Jun 2020 23:26:01: 27000000 INFO @ Fri, 26 Jun 2020 23:26:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.10_summits.bed INFO @ Fri, 26 Jun 2020 23:26:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (802 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:26:06: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:26:06: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:26:06: #1 total tags in treatment: 12961504 INFO @ Fri, 26 Jun 2020 23:26:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:26:06: #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 23:26:06: #1 tags after filtering in treatment: 10734218 INFO @ Fri, 26 Jun 2020 23:26:06: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 23:26:06: #1 finished! INFO @ Fri, 26 Jun 2020 23:26:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:26:07: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 23:26:07: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 23:26:07: start model_add_line... INFO @ Fri, 26 Jun 2020 23:26:07: start X-correlation... INFO @ Fri, 26 Jun 2020 23:26:07: end of X-cor INFO @ Fri, 26 Jun 2020 23:26:07: #2 finished! INFO @ Fri, 26 Jun 2020 23:26:07: #2 predicted fragment length is 127 bps INFO @ Fri, 26 Jun 2020 23:26:07: #2 alternative fragment length(s) may be 4,127 bps INFO @ Fri, 26 Jun 2020 23:26:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.20_model.r INFO @ Fri, 26 Jun 2020 23:26:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:26:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:26:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085428/SRX4085428.20_summits.bed INFO @ Fri, 26 Jun 2020 23:26:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 1 millis CompletedMACS2peakCalling