Job ID = 6497376 SRX = SRX4085338 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:43:04 prefetch.2.10.7: 1) Downloading 'SRR7167367'... 2020-06-25T21:43:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:48:31 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:48:31 prefetch.2.10.7: 1) 'SRR7167367' was downloaded successfully Read 31421314 spots for SRR7167367/SRR7167367.sra Written 31421314 spots for SRR7167367/SRR7167367.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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:12 31421314 reads; of these: 31421314 (100.00%) were paired; of these: 3630845 (11.56%) aligned concordantly 0 times 24945693 (79.39%) aligned concordantly exactly 1 time 2844776 (9.05%) aligned concordantly >1 times ---- 3630845 pairs aligned concordantly 0 times; of these: 252284 (6.95%) aligned discordantly 1 time ---- 3378561 pairs aligned 0 times concordantly or discordantly; of these: 6757122 mates make up the pairs; of these: 5277273 (78.10%) aligned 0 times 1234023 (18.26%) aligned exactly 1 time 245826 (3.64%) aligned >1 times 91.60% overall alignment rate Time searching: 00:26:14 Overall time: 00:26:15 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 24 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] 17620825 / 28012502 = 0.6290 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 07:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.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 07:34:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:34:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:34:23: 1000000 INFO @ Fri, 26 Jun 2020 07:34:28: 2000000 INFO @ Fri, 26 Jun 2020 07:34:34: 3000000 INFO @ Fri, 26 Jun 2020 07:34:39: 4000000 INFO @ Fri, 26 Jun 2020 07:34:44: 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 07:34:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.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 07:34:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:34:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:34:50: 6000000 INFO @ Fri, 26 Jun 2020 07:34:53: 1000000 INFO @ Fri, 26 Jun 2020 07:34:55: 7000000 INFO @ Fri, 26 Jun 2020 07:34:58: 2000000 INFO @ Fri, 26 Jun 2020 07:35:01: 8000000 INFO @ Fri, 26 Jun 2020 07:35:04: 3000000 INFO @ Fri, 26 Jun 2020 07:35:06: 9000000 INFO @ Fri, 26 Jun 2020 07:35:09: 4000000 INFO @ Fri, 26 Jun 2020 07:35:12: 10000000 INFO @ Fri, 26 Jun 2020 07:35:15: 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 07:35:17: 11000000 INFO @ Fri, 26 Jun 2020 07:35:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.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 07:35:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:35:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:35:20: 6000000 INFO @ Fri, 26 Jun 2020 07:35:23: 12000000 INFO @ Fri, 26 Jun 2020 07:35:24: 1000000 INFO @ Fri, 26 Jun 2020 07:35:26: 7000000 INFO @ Fri, 26 Jun 2020 07:35:28: 13000000 INFO @ Fri, 26 Jun 2020 07:35:30: 2000000 INFO @ Fri, 26 Jun 2020 07:35:31: 8000000 INFO @ Fri, 26 Jun 2020 07:35:34: 14000000 INFO @ Fri, 26 Jun 2020 07:35:37: 3000000 INFO @ Fri, 26 Jun 2020 07:35:37: 9000000 INFO @ Fri, 26 Jun 2020 07:35:40: 15000000 INFO @ Fri, 26 Jun 2020 07:35:43: 10000000 INFO @ Fri, 26 Jun 2020 07:35:43: 4000000 INFO @ Fri, 26 Jun 2020 07:35:45: 16000000 INFO @ Fri, 26 Jun 2020 07:35:48: 11000000 INFO @ Fri, 26 Jun 2020 07:35:49: 5000000 INFO @ Fri, 26 Jun 2020 07:35:51: 17000000 INFO @ Fri, 26 Jun 2020 07:35:54: 12000000 INFO @ Fri, 26 Jun 2020 07:35:56: 6000000 INFO @ Fri, 26 Jun 2020 07:35:57: 18000000 INFO @ Fri, 26 Jun 2020 07:35:59: 13000000 INFO @ Fri, 26 Jun 2020 07:36:02: 7000000 INFO @ Fri, 26 Jun 2020 07:36:02: 19000000 INFO @ Fri, 26 Jun 2020 07:36:05: 14000000 INFO @ Fri, 26 Jun 2020 07:36:08: 20000000 INFO @ Fri, 26 Jun 2020 07:36:08: 8000000 INFO @ Fri, 26 Jun 2020 07:36:10: 15000000 INFO @ Fri, 26 Jun 2020 07:36:13: 21000000 INFO @ Fri, 26 Jun 2020 07:36:14: 9000000 INFO @ Fri, 26 Jun 2020 07:36:16: 16000000 INFO @ Fri, 26 Jun 2020 07:36:18: 22000000 INFO @ Fri, 26 Jun 2020 07:36:20: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:36:20: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:36:20: #1 total tags in treatment: 10268829 INFO @ Fri, 26 Jun 2020 07:36:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:36:20: #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 07:36:20: #1 tags after filtering in treatment: 8699429 INFO @ Fri, 26 Jun 2020 07:36:20: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 07:36:20: #1 finished! INFO @ Fri, 26 Jun 2020 07:36:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:36:21: #2 number of paired peaks: 412 WARNING @ Fri, 26 Jun 2020 07:36:21: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Fri, 26 Jun 2020 07:36:21: start model_add_line... INFO @ Fri, 26 Jun 2020 07:36:21: start X-correlation... INFO @ Fri, 26 Jun 2020 07:36:21: end of X-cor INFO @ Fri, 26 Jun 2020 07:36:21: #2 finished! INFO @ Fri, 26 Jun 2020 07:36:21: #2 predicted fragment length is 112 bps INFO @ Fri, 26 Jun 2020 07:36:21: #2 alternative fragment length(s) may be 4,112,124 bps INFO @ Fri, 26 Jun 2020 07:36:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.05_model.r INFO @ Fri, 26 Jun 2020 07:36:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:36:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:36:21: 10000000 INFO @ Fri, 26 Jun 2020 07:36:21: 17000000 INFO @ Fri, 26 Jun 2020 07:36:27: 18000000 INFO @ Fri, 26 Jun 2020 07:36:27: 11000000 INFO @ Fri, 26 Jun 2020 07:36:32: 19000000 INFO @ Fri, 26 Jun 2020 07:36:33: 12000000 INFO @ Fri, 26 Jun 2020 07:36:37: 20000000 INFO @ Fri, 26 Jun 2020 07:36:40: 13000000 INFO @ Fri, 26 Jun 2020 07:36:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:36:42: 21000000 INFO @ Fri, 26 Jun 2020 07:36:46: 14000000 INFO @ Fri, 26 Jun 2020 07:36:48: 22000000 INFO @ Fri, 26 Jun 2020 07:36:49: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:36:49: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:36:49: #1 total tags in treatment: 10268829 INFO @ Fri, 26 Jun 2020 07:36:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:36:49: #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 07:36:49: #1 tags after filtering in treatment: 8699429 INFO @ Fri, 26 Jun 2020 07:36:49: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 07:36:49: #1 finished! INFO @ Fri, 26 Jun 2020 07:36:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.05_summits.bed INFO @ Fri, 26 Jun 2020 07:36:50: Done! INFO @ Fri, 26 Jun 2020 07:36:50: #2 number of paired peaks: 412 WARNING @ Fri, 26 Jun 2020 07:36:50: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Fri, 26 Jun 2020 07:36:50: start model_add_line... INFO @ Fri, 26 Jun 2020 07:36:50: start X-correlation... INFO @ Fri, 26 Jun 2020 07:36:50: end of X-cor INFO @ Fri, 26 Jun 2020 07:36:50: #2 finished! INFO @ Fri, 26 Jun 2020 07:36:50: #2 predicted fragment length is 112 bps INFO @ Fri, 26 Jun 2020 07:36:50: #2 alternative fragment length(s) may be 4,112,124 bps INFO @ Fri, 26 Jun 2020 07:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.10_model.r INFO @ Fri, 26 Jun 2020 07:36:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:36:50: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (512 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:36:52: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:36:58: 16000000 INFO @ Fri, 26 Jun 2020 07:37:04: 17000000 INFO @ Fri, 26 Jun 2020 07:37:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:37:10: 18000000 INFO @ Fri, 26 Jun 2020 07:37:16: 19000000 INFO @ Fri, 26 Jun 2020 07:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.10_summits.bed INFO @ Fri, 26 Jun 2020 07:37:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:37:21: 20000000 INFO @ Fri, 26 Jun 2020 07:37:27: 21000000 INFO @ Fri, 26 Jun 2020 07:37:33: 22000000 INFO @ Fri, 26 Jun 2020 07:37:34: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:37:34: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:37:34: #1 total tags in treatment: 10268829 INFO @ Fri, 26 Jun 2020 07:37:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:37:34: #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 07:37:35: #1 tags after filtering in treatment: 8699429 INFO @ Fri, 26 Jun 2020 07:37:35: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 07:37:35: #1 finished! INFO @ Fri, 26 Jun 2020 07:37:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:37:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:37:35: #2 number of paired peaks: 412 WARNING @ Fri, 26 Jun 2020 07:37:35: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Fri, 26 Jun 2020 07:37:35: start model_add_line... INFO @ Fri, 26 Jun 2020 07:37:35: start X-correlation... INFO @ Fri, 26 Jun 2020 07:37:35: end of X-cor INFO @ Fri, 26 Jun 2020 07:37:35: #2 finished! INFO @ Fri, 26 Jun 2020 07:37:35: #2 predicted fragment length is 112 bps INFO @ Fri, 26 Jun 2020 07:37:35: #2 alternative fragment length(s) may be 4,112,124 bps INFO @ Fri, 26 Jun 2020 07:37:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.20_model.r INFO @ Fri, 26 Jun 2020 07:37:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:37:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:37:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:38:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:38:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:38:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085338/SRX4085338.20_summits.bed INFO @ Fri, 26 Jun 2020 07:38:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 7 millis CompletedMACS2peakCalling