Job ID = 10845159 sra ファイルのダウンロード中... Completed: 1710461K bytes transferred in 25 seconds (551283K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 25917677 spots for /home/okishinya/chipatlas/results/ce10/SRX4085435/SRR7167464.sra Written 25917677 spots for /home/okishinya/chipatlas/results/ce10/SRX4085435/SRR7167464.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:23 25917677 reads; of these: 25917677 (100.00%) were paired; of these: 12013946 (46.35%) aligned concordantly 0 times 11872490 (45.81%) aligned concordantly exactly 1 time 2031241 (7.84%) aligned concordantly >1 times ---- 12013946 pairs aligned concordantly 0 times; of these: 156520 (1.30%) aligned discordantly 1 time ---- 11857426 pairs aligned 0 times concordantly or discordantly; of these: 23714852 mates make up the pairs; of these: 20608461 (86.90%) aligned 0 times 2679662 (11.30%) aligned exactly 1 time 426729 (1.80%) aligned >1 times 60.24% overall alignment rate Time searching: 00:18:25 Overall time: 00:18:25 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 16 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] 2615335 / 14017747 = 0.1866 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Wed, 04 Jul 2018 09:56:16: # Command line: callpeak -t SRX4085435.bam -f BAM -g ce -n SRX4085435.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085435.10 # format = BAM # ChIP-seq file = ['SRX4085435.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 @ Wed, 04 Jul 2018 09:56:16: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:56:16: # Command line: callpeak -t SRX4085435.bam -f BAM -g ce -n SRX4085435.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085435.20 # format = BAM # ChIP-seq file = ['SRX4085435.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 @ Wed, 04 Jul 2018 09:56:16: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:56:16: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:56:16: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:56:16: # Command line: callpeak -t SRX4085435.bam -f BAM -g ce -n SRX4085435.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085435.05 # format = BAM # ChIP-seq file = ['SRX4085435.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 @ Wed, 04 Jul 2018 09:56:16: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:56:16: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:56:22: 1000000 INFO @ Wed, 04 Jul 2018 09:56:22: 1000000 INFO @ Wed, 04 Jul 2018 09:56:22: 1000000 INFO @ Wed, 04 Jul 2018 09:56:28: 2000000 INFO @ Wed, 04 Jul 2018 09:56:29: 2000000 INFO @ Wed, 04 Jul 2018 09:56:29: 2000000 INFO @ Wed, 04 Jul 2018 09:56:35: 3000000 INFO @ Wed, 04 Jul 2018 09:56:36: 3000000 INFO @ Wed, 04 Jul 2018 09:56:36: 3000000 INFO @ Wed, 04 Jul 2018 09:56:41: 4000000 INFO @ Wed, 04 Jul 2018 09:56:42: 4000000 INFO @ Wed, 04 Jul 2018 09:56:42: 4000000 INFO @ Wed, 04 Jul 2018 09:56:47: 5000000 INFO @ Wed, 04 Jul 2018 09:56:49: 5000000 INFO @ Wed, 04 Jul 2018 09:56:49: 5000000 INFO @ Wed, 04 Jul 2018 09:56:53: 6000000 INFO @ Wed, 04 Jul 2018 09:56:56: 6000000 INFO @ Wed, 04 Jul 2018 09:56:56: 6000000 INFO @ Wed, 04 Jul 2018 09:56:59: 7000000 INFO @ Wed, 04 Jul 2018 09:57:02: 7000000 INFO @ Wed, 04 Jul 2018 09:57:03: 7000000 INFO @ Wed, 04 Jul 2018 09:57:06: 8000000 INFO @ Wed, 04 Jul 2018 09:57:09: 8000000 INFO @ Wed, 04 Jul 2018 09:57:09: 8000000 INFO @ Wed, 04 Jul 2018 09:57:12: 9000000 INFO @ Wed, 04 Jul 2018 09:57:16: 9000000 INFO @ Wed, 04 Jul 2018 09:57:16: 9000000 INFO @ Wed, 04 Jul 2018 09:57:18: 10000000 INFO @ Wed, 04 Jul 2018 09:57:22: 10000000 INFO @ Wed, 04 Jul 2018 09:57:23: 10000000 INFO @ Wed, 04 Jul 2018 09:57:25: 11000000 INFO @ Wed, 04 Jul 2018 09:57:29: 11000000 INFO @ Wed, 04 Jul 2018 09:57:29: 11000000 INFO @ Wed, 04 Jul 2018 09:57:31: 12000000 INFO @ Wed, 04 Jul 2018 09:57:35: 12000000 INFO @ Wed, 04 Jul 2018 09:57:36: 12000000 INFO @ Wed, 04 Jul 2018 09:57:38: 13000000 INFO @ Wed, 04 Jul 2018 09:57:41: 13000000 INFO @ Wed, 04 Jul 2018 09:57:43: 13000000 INFO @ Wed, 04 Jul 2018 09:57:44: 14000000 INFO @ Wed, 04 Jul 2018 09:57:48: 14000000 INFO @ Wed, 04 Jul 2018 09:57:50: 14000000 INFO @ Wed, 04 Jul 2018 09:57:50: 15000000 INFO @ Wed, 04 Jul 2018 09:57:55: 15000000 INFO @ Wed, 04 Jul 2018 09:57:56: 15000000 INFO @ Wed, 04 Jul 2018 09:57:57: 16000000 INFO @ Wed, 04 Jul 2018 09:58:01: 16000000 INFO @ Wed, 04 Jul 2018 09:58:03: 16000000 INFO @ Wed, 04 Jul 2018 09:58:03: 17000000 INFO @ Wed, 04 Jul 2018 09:58:07: 17000000 INFO @ Wed, 04 Jul 2018 09:58:10: 18000000 INFO @ Wed, 04 Jul 2018 09:58:10: 17000000 INFO @ Wed, 04 Jul 2018 09:58:14: 18000000 INFO @ Wed, 04 Jul 2018 09:58:16: 19000000 INFO @ Wed, 04 Jul 2018 09:58:16: 18000000 INFO @ Wed, 04 Jul 2018 09:58:20: 19000000 INFO @ Wed, 04 Jul 2018 09:58:23: 20000000 INFO @ Wed, 04 Jul 2018 09:58:23: 19000000 INFO @ Wed, 04 Jul 2018 09:58:27: 20000000 INFO @ Wed, 04 Jul 2018 09:58:29: 21000000 INFO @ Wed, 04 Jul 2018 09:58:30: 20000000 INFO @ Wed, 04 Jul 2018 09:58:33: 21000000 INFO @ Wed, 04 Jul 2018 09:58:35: 22000000 INFO @ Wed, 04 Jul 2018 09:58:37: 21000000 INFO @ Wed, 04 Jul 2018 09:58:40: 22000000 INFO @ Wed, 04 Jul 2018 09:58:42: 23000000 INFO @ Wed, 04 Jul 2018 09:58:43: 22000000 INFO @ Wed, 04 Jul 2018 09:58:46: 23000000 INFO @ Wed, 04 Jul 2018 09:58:48: 24000000 INFO @ Wed, 04 Jul 2018 09:58:50: 23000000 INFO @ Wed, 04 Jul 2018 09:58:53: 24000000 INFO @ Wed, 04 Jul 2018 09:58:54: 25000000 INFO @ Wed, 04 Jul 2018 09:58:57: 24000000 INFO @ Wed, 04 Jul 2018 09:58:59: 25000000 INFO @ Wed, 04 Jul 2018 09:59:00: #1 tag size is determined as 51 bps INFO @ Wed, 04 Jul 2018 09:59:00: #1 tag size = 51 INFO @ Wed, 04 Jul 2018 09:59:00: #1 total tags in treatment: 11304298 INFO @ Wed, 04 Jul 2018 09:59:00: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:59:01: #1 tags after filtering in treatment: 10324755 INFO @ Wed, 04 Jul 2018 09:59:01: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 04 Jul 2018 09:59:01: #1 finished! INFO @ Wed, 04 Jul 2018 09:59:01: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:59:01: #2 number of paired peaks: 359 WARNING @ Wed, 04 Jul 2018 09:59:01: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Wed, 04 Jul 2018 09:59:01: start model_add_line... INFO @ Wed, 04 Jul 2018 09:59:02: start X-correlation... INFO @ Wed, 04 Jul 2018 09:59:02: end of X-cor INFO @ Wed, 04 Jul 2018 09:59:02: #2 finished! INFO @ Wed, 04 Jul 2018 09:59:02: #2 predicted fragment length is 136 bps INFO @ Wed, 04 Jul 2018 09:59:02: #2 alternative fragment length(s) may be 4,136 bps INFO @ Wed, 04 Jul 2018 09:59:02: #2.2 Generate R script for model : SRX4085435.10_model.r INFO @ Wed, 04 Jul 2018 09:59:02: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:59:03: 25000000 INFO @ Wed, 04 Jul 2018 09:59:05: #1 tag size is determined as 51 bps INFO @ Wed, 04 Jul 2018 09:59:05: #1 tag size = 51 INFO @ Wed, 04 Jul 2018 09:59:05: #1 total tags in treatment: 11304298 INFO @ Wed, 04 Jul 2018 09:59:05: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:59:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:59:05: #1 tags after filtering in treatment: 10324755 INFO @ Wed, 04 Jul 2018 09:59:05: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 04 Jul 2018 09:59:05: #1 finished! INFO @ Wed, 04 Jul 2018 09:59:05: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:59:06: #2 number of paired peaks: 359 WARNING @ Wed, 04 Jul 2018 09:59:06: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Wed, 04 Jul 2018 09:59:06: start model_add_line... INFO @ Wed, 04 Jul 2018 09:59:06: start X-correlation... INFO @ Wed, 04 Jul 2018 09:59:06: end of X-cor INFO @ Wed, 04 Jul 2018 09:59:06: #2 finished! INFO @ Wed, 04 Jul 2018 09:59:06: #2 predicted fragment length is 136 bps INFO @ Wed, 04 Jul 2018 09:59:06: #2 alternative fragment length(s) may be 4,136 bps INFO @ Wed, 04 Jul 2018 09:59:06: #2.2 Generate R script for model : SRX4085435.20_model.r INFO @ Wed, 04 Jul 2018 09:59:06: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:59:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:59:10: #1 tag size is determined as 51 bps INFO @ Wed, 04 Jul 2018 09:59:10: #1 tag size = 51 INFO @ Wed, 04 Jul 2018 09:59:10: #1 total tags in treatment: 11304298 INFO @ Wed, 04 Jul 2018 09:59:10: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:59:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:59:10: #1 tags after filtering in treatment: 10324755 INFO @ Wed, 04 Jul 2018 09:59:10: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 04 Jul 2018 09:59:10: #1 finished! INFO @ Wed, 04 Jul 2018 09:59:10: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:59:10: #2 number of paired peaks: 359 WARNING @ Wed, 04 Jul 2018 09:59:10: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Wed, 04 Jul 2018 09:59:10: start model_add_line... INFO @ Wed, 04 Jul 2018 09:59:11: start X-correlation... INFO @ Wed, 04 Jul 2018 09:59:11: end of X-cor INFO @ Wed, 04 Jul 2018 09:59:11: #2 finished! INFO @ Wed, 04 Jul 2018 09:59:11: #2 predicted fragment length is 136 bps INFO @ Wed, 04 Jul 2018 09:59:11: #2 alternative fragment length(s) may be 4,136 bps INFO @ Wed, 04 Jul 2018 09:59:11: #2.2 Generate R script for model : SRX4085435.05_model.r INFO @ Wed, 04 Jul 2018 09:59:11: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:59:24: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:59:29: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:59:33: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:59:35: #4 Write output xls file... SRX4085435.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:59:35: #4 Write peak in narrowPeak format file... SRX4085435.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:59:35: #4 Write summits bed file... SRX4085435.10_summits.bed INFO @ Wed, 04 Jul 2018 09:59:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (297 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:59:40: #4 Write output xls file... SRX4085435.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:59:40: #4 Write peak in narrowPeak format file... SRX4085435.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:59:40: #4 Write summits bed file... SRX4085435.20_summits.bed INFO @ Wed, 04 Jul 2018 09:59:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:59:44: #4 Write output xls file... SRX4085435.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:59:44: #4 Write peak in narrowPeak format file... SRX4085435.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:59:44: #4 Write summits bed file... SRX4085435.05_summits.bed INFO @ Wed, 04 Jul 2018 09:59:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (453 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。