Job ID = 10845158 sra ファイルのダウンロード中... Completed: 1375525K bytes transferred in 21 seconds (522570K 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 19278998 spots for /home/okishinya/chipatlas/results/ce10/SRX4085405/SRR7167434.sra Written 19278998 spots for /home/okishinya/chipatlas/results/ce10/SRX4085405/SRR7167434.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:30 19278998 reads; of these: 19278998 (100.00%) were paired; of these: 869212 (4.51%) aligned concordantly 0 times 16344058 (84.78%) aligned concordantly exactly 1 time 2065728 (10.71%) aligned concordantly >1 times ---- 869212 pairs aligned concordantly 0 times; of these: 238916 (27.49%) aligned discordantly 1 time ---- 630296 pairs aligned 0 times concordantly or discordantly; of these: 1260592 mates make up the pairs; of these: 710805 (56.39%) aligned 0 times 430871 (34.18%) aligned exactly 1 time 118916 (9.43%) aligned >1 times 98.16% overall alignment rate Time searching: 00:18:30 Overall time: 00:18:30 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] 5596043 / 18554599 = 0.3016 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 09:56:27: # Command line: callpeak -t SRX4085405.bam -f BAM -g ce -n SRX4085405.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085405.05 # format = BAM # ChIP-seq file = ['SRX4085405.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 09:56:27: # Command line: callpeak -t SRX4085405.bam -f BAM -g ce -n SRX4085405.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085405.10 # format = BAM # ChIP-seq file = ['SRX4085405.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 09:56:27: # Command line: callpeak -t SRX4085405.bam -f BAM -g ce -n SRX4085405.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085405.20 # format = BAM # ChIP-seq file = ['SRX4085405.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 09:56:27: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:56:27: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:56:27: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:56:27: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:56:27: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:56:27: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:56:33: 1000000 INFO @ Wed, 04 Jul 2018 09:56:33: 1000000 INFO @ Wed, 04 Jul 2018 09:56:33: 1000000 INFO @ Wed, 04 Jul 2018 09:56:40: 2000000 INFO @ Wed, 04 Jul 2018 09:56:40: 2000000 INFO @ Wed, 04 Jul 2018 09:56:40: 2000000 INFO @ Wed, 04 Jul 2018 09:56:47: 3000000 INFO @ Wed, 04 Jul 2018 09:56:47: 3000000 INFO @ Wed, 04 Jul 2018 09:56:48: 3000000 INFO @ Wed, 04 Jul 2018 09:56:53: 4000000 INFO @ Wed, 04 Jul 2018 09:56:53: 4000000 INFO @ Wed, 04 Jul 2018 09:56:57: 4000000 INFO @ Wed, 04 Jul 2018 09:57:00: 5000000 INFO @ Wed, 04 Jul 2018 09:57:00: 5000000 INFO @ Wed, 04 Jul 2018 09:57:06: 5000000 INFO @ Wed, 04 Jul 2018 09:57:07: 6000000 INFO @ Wed, 04 Jul 2018 09:57:07: 6000000 INFO @ Wed, 04 Jul 2018 09:57:14: 7000000 INFO @ Wed, 04 Jul 2018 09:57:14: 7000000 INFO @ Wed, 04 Jul 2018 09:57:14: 6000000 INFO @ Wed, 04 Jul 2018 09:57:21: 8000000 INFO @ Wed, 04 Jul 2018 09:57:21: 8000000 INFO @ Wed, 04 Jul 2018 09:57:23: 7000000 INFO @ Wed, 04 Jul 2018 09:57:28: 9000000 INFO @ Wed, 04 Jul 2018 09:57:28: 9000000 INFO @ Wed, 04 Jul 2018 09:57:32: 8000000 INFO @ Wed, 04 Jul 2018 09:57:35: 10000000 INFO @ Wed, 04 Jul 2018 09:57:35: 10000000 INFO @ Wed, 04 Jul 2018 09:57:40: 9000000 INFO @ Wed, 04 Jul 2018 09:57:41: 11000000 INFO @ Wed, 04 Jul 2018 09:57:42: 11000000 INFO @ Wed, 04 Jul 2018 09:57:48: 12000000 INFO @ Wed, 04 Jul 2018 09:57:48: 12000000 INFO @ Wed, 04 Jul 2018 09:57:49: 10000000 INFO @ Wed, 04 Jul 2018 09:57:55: 13000000 INFO @ Wed, 04 Jul 2018 09:57:55: 13000000 INFO @ Wed, 04 Jul 2018 09:57:58: 11000000 INFO @ Wed, 04 Jul 2018 09:58:02: 14000000 INFO @ Wed, 04 Jul 2018 09:58:02: 14000000 INFO @ Wed, 04 Jul 2018 09:58:06: 12000000 INFO @ Wed, 04 Jul 2018 09:58:09: 15000000 INFO @ Wed, 04 Jul 2018 09:58:09: 15000000 INFO @ Wed, 04 Jul 2018 09:58:15: 13000000 INFO @ Wed, 04 Jul 2018 09:58:16: 16000000 INFO @ Wed, 04 Jul 2018 09:58:16: 16000000 INFO @ Wed, 04 Jul 2018 09:58:23: 17000000 INFO @ Wed, 04 Jul 2018 09:58:23: 17000000 INFO @ Wed, 04 Jul 2018 09:58:24: 14000000 INFO @ Wed, 04 Jul 2018 09:58:30: 18000000 INFO @ Wed, 04 Jul 2018 09:58:30: 18000000 INFO @ Wed, 04 Jul 2018 09:58:32: 15000000 INFO @ Wed, 04 Jul 2018 09:58:37: 19000000 INFO @ Wed, 04 Jul 2018 09:58:37: 19000000 INFO @ Wed, 04 Jul 2018 09:58:41: 16000000 INFO @ Wed, 04 Jul 2018 09:58:44: 20000000 INFO @ Wed, 04 Jul 2018 09:58:44: 20000000 INFO @ Wed, 04 Jul 2018 09:58:50: 17000000 INFO @ Wed, 04 Jul 2018 09:58:50: 21000000 INFO @ Wed, 04 Jul 2018 09:58:51: 21000000 INFO @ Wed, 04 Jul 2018 09:58:57: 22000000 INFO @ Wed, 04 Jul 2018 09:58:58: 22000000 INFO @ Wed, 04 Jul 2018 09:58:58: 18000000 INFO @ Wed, 04 Jul 2018 09:59:04: 23000000 INFO @ Wed, 04 Jul 2018 09:59:05: 23000000 INFO @ Wed, 04 Jul 2018 09:59:07: 19000000 INFO @ Wed, 04 Jul 2018 09:59:11: 24000000 INFO @ Wed, 04 Jul 2018 09:59:12: 24000000 INFO @ Wed, 04 Jul 2018 09:59:16: 20000000 INFO @ Wed, 04 Jul 2018 09:59:18: 25000000 INFO @ Wed, 04 Jul 2018 09:59:19: 25000000 INFO @ Wed, 04 Jul 2018 09:59:24: 21000000 INFO @ Wed, 04 Jul 2018 09:59:26: 26000000 INFO @ Wed, 04 Jul 2018 09:59:26: 26000000 INFO @ Wed, 04 Jul 2018 09:59:30: #1 tag size is determined as 51 bps INFO @ Wed, 04 Jul 2018 09:59:30: #1 tag size = 51 INFO @ Wed, 04 Jul 2018 09:59:30: #1 total tags in treatment: 12841614 INFO @ Wed, 04 Jul 2018 09:59:30: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:59:30: #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 09:59:30: #1 tags after filtering in treatment: 11021016 INFO @ Wed, 04 Jul 2018 09:59:30: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 09:59:30: #1 finished! INFO @ Wed, 04 Jul 2018 09:59:30: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:59:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:59:31: #1 tag size is determined as 51 bps INFO @ Wed, 04 Jul 2018 09:59:31: #1 tag size = 51 INFO @ Wed, 04 Jul 2018 09:59:31: #1 total tags in treatment: 12841614 INFO @ Wed, 04 Jul 2018 09:59:31: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:59:31: #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 09:59:31: #1 tags after filtering in treatment: 11021016 INFO @ Wed, 04 Jul 2018 09:59:31: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 09:59:31: #1 finished! INFO @ Wed, 04 Jul 2018 09:59:31: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:59:31: #2 number of paired peaks: 190 WARNING @ Wed, 04 Jul 2018 09:59:31: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 04 Jul 2018 09:59:31: start model_add_line... INFO @ Wed, 04 Jul 2018 09:59:31: start X-correlation... INFO @ Wed, 04 Jul 2018 09:59:32: end of X-cor INFO @ Wed, 04 Jul 2018 09:59:32: #2 finished! INFO @ Wed, 04 Jul 2018 09:59:32: #2 predicted fragment length is 94 bps INFO @ Wed, 04 Jul 2018 09:59:32: #2 alternative fragment length(s) may be 3,94,111,598 bps INFO @ Wed, 04 Jul 2018 09:59:32: #2.2 Generate R script for model : SRX4085405.05_model.r WARNING @ Wed, 04 Jul 2018 09:59:32: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:59:32: #2 You may need to consider one of the other alternative d(s): 3,94,111,598 WARNING @ Wed, 04 Jul 2018 09:59:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:59:32: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:59:32: #2 number of paired peaks: 190 WARNING @ Wed, 04 Jul 2018 09:59:32: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 04 Jul 2018 09:59:32: start model_add_line... INFO @ Wed, 04 Jul 2018 09:59:32: start X-correlation... INFO @ Wed, 04 Jul 2018 09:59:32: end of X-cor INFO @ Wed, 04 Jul 2018 09:59:32: #2 finished! INFO @ Wed, 04 Jul 2018 09:59:32: #2 predicted fragment length is 94 bps INFO @ Wed, 04 Jul 2018 09:59:32: #2 alternative fragment length(s) may be 3,94,111,598 bps INFO @ Wed, 04 Jul 2018 09:59:32: #2.2 Generate R script for model : SRX4085405.10_model.r WARNING @ Wed, 04 Jul 2018 09:59:32: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:59:32: #2 You may need to consider one of the other alternative d(s): 3,94,111,598 WARNING @ Wed, 04 Jul 2018 09:59:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:59:32: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:59:33: 22000000 INFO @ Wed, 04 Jul 2018 09:59:41: 23000000 INFO @ Wed, 04 Jul 2018 09:59:49: 24000000 INFO @ Wed, 04 Jul 2018 09:59:56: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:59:57: 25000000 INFO @ Wed, 04 Jul 2018 09:59:57: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:00:05: 26000000 INFO @ Wed, 04 Jul 2018 10:00:08: #4 Write output xls file... SRX4085405.10_peaks.xls INFO @ Wed, 04 Jul 2018 10:00:08: #4 Write peak in narrowPeak format file... SRX4085405.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:00:08: #4 Write summits bed file... SRX4085405.10_summits.bed INFO @ Wed, 04 Jul 2018 10:00:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1450 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 10:00:10: #4 Write output xls file... SRX4085405.05_peaks.xls INFO @ Wed, 04 Jul 2018 10:00:10: #4 Write peak in narrowPeak format file... SRX4085405.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:00:10: #4 Write summits bed file... SRX4085405.05_summits.bed INFO @ Wed, 04 Jul 2018 10:00:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3906 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 10:00:11: #1 tag size is determined as 51 bps INFO @ Wed, 04 Jul 2018 10:00:11: #1 tag size = 51 INFO @ Wed, 04 Jul 2018 10:00:11: #1 total tags in treatment: 12841614 INFO @ Wed, 04 Jul 2018 10:00:11: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 10:00:11: #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 10:00:11: #1 tags after filtering in treatment: 11021016 INFO @ Wed, 04 Jul 2018 10:00:11: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 10:00:11: #1 finished! INFO @ Wed, 04 Jul 2018 10:00:11: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 10:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 10:00:12: #2 number of paired peaks: 190 WARNING @ Wed, 04 Jul 2018 10:00:12: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Wed, 04 Jul 2018 10:00:12: start model_add_line... INFO @ Wed, 04 Jul 2018 10:00:12: start X-correlation... INFO @ Wed, 04 Jul 2018 10:00:12: end of X-cor INFO @ Wed, 04 Jul 2018 10:00:12: #2 finished! INFO @ Wed, 04 Jul 2018 10:00:12: #2 predicted fragment length is 94 bps INFO @ Wed, 04 Jul 2018 10:00:12: #2 alternative fragment length(s) may be 3,94,111,598 bps INFO @ Wed, 04 Jul 2018 10:00:12: #2.2 Generate R script for model : SRX4085405.20_model.r WARNING @ Wed, 04 Jul 2018 10:00:12: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 10:00:12: #2 You may need to consider one of the other alternative d(s): 3,94,111,598 WARNING @ Wed, 04 Jul 2018 10:00:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 10:00:12: #3 Call peaks... INFO @ Wed, 04 Jul 2018 10:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 10:00:38: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 10:00:51: #4 Write output xls file... SRX4085405.20_peaks.xls INFO @ Wed, 04 Jul 2018 10:00:51: #4 Write peak in narrowPeak format file... SRX4085405.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 10:00:51: #4 Write summits bed file... SRX4085405.20_summits.bed INFO @ Wed, 04 Jul 2018 10:00:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (249 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。