Job ID = 4178462 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-05T03:31:20 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-05T03:31:20 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-05T03:38:53 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 18,541,787 reads read : 37,083,574 reads written : 37,083,574 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:30:10 18541787 reads; of these: 18541787 (100.00%) were paired; of these: 2918580 (15.74%) aligned concordantly 0 times 14085205 (75.96%) aligned concordantly exactly 1 time 1538002 (8.29%) aligned concordantly >1 times ---- 2918580 pairs aligned concordantly 0 times; of these: 340415 (11.66%) aligned discordantly 1 time ---- 2578165 pairs aligned 0 times concordantly or discordantly; of these: 5156330 mates make up the pairs; of these: 4481900 (86.92%) aligned 0 times 506128 (9.82%) aligned exactly 1 time 168302 (3.26%) aligned >1 times 87.91% overall alignment rate Time searching: 00:30:10 Overall time: 00:30:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1953590 / 15926803 = 0.1227 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:24:40: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:24:40: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:24:50: 1000000 INFO @ Thu, 05 Dec 2019 13:24:59: 2000000 INFO @ Thu, 05 Dec 2019 13:25:10: 3000000 INFO @ Thu, 05 Dec 2019 13:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:25:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:25:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:25:19: 1000000 INFO @ Thu, 05 Dec 2019 13:25:21: 4000000 INFO @ Thu, 05 Dec 2019 13:25:27: 2000000 INFO @ Thu, 05 Dec 2019 13:25:30: 5000000 INFO @ Thu, 05 Dec 2019 13:25:35: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:25:40: 6000000 INFO @ Thu, 05 Dec 2019 13:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:25:40: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:25:40: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:25:43: 4000000 INFO @ Thu, 05 Dec 2019 13:25:49: 7000000 INFO @ Thu, 05 Dec 2019 13:25:50: 1000000 INFO @ Thu, 05 Dec 2019 13:25:51: 5000000 INFO @ Thu, 05 Dec 2019 13:25:59: 6000000 INFO @ Thu, 05 Dec 2019 13:25:59: 8000000 INFO @ Thu, 05 Dec 2019 13:25:59: 2000000 INFO @ Thu, 05 Dec 2019 13:26:07: 7000000 INFO @ Thu, 05 Dec 2019 13:26:08: 9000000 INFO @ Thu, 05 Dec 2019 13:26:09: 3000000 INFO @ Thu, 05 Dec 2019 13:26:15: 8000000 INFO @ Thu, 05 Dec 2019 13:26:18: 10000000 INFO @ Thu, 05 Dec 2019 13:26:19: 4000000 INFO @ Thu, 05 Dec 2019 13:26:23: 9000000 INFO @ Thu, 05 Dec 2019 13:26:28: 11000000 INFO @ Thu, 05 Dec 2019 13:26:29: 5000000 INFO @ Thu, 05 Dec 2019 13:26:31: 10000000 INFO @ Thu, 05 Dec 2019 13:26:38: 12000000 INFO @ Thu, 05 Dec 2019 13:26:38: 6000000 INFO @ Thu, 05 Dec 2019 13:26:39: 11000000 INFO @ Thu, 05 Dec 2019 13:26:47: 13000000 INFO @ Thu, 05 Dec 2019 13:26:47: 12000000 INFO @ Thu, 05 Dec 2019 13:26:48: 7000000 INFO @ Thu, 05 Dec 2019 13:26:55: 13000000 INFO @ Thu, 05 Dec 2019 13:26:56: 14000000 INFO @ Thu, 05 Dec 2019 13:26:58: 8000000 INFO @ Thu, 05 Dec 2019 13:27:03: 14000000 INFO @ Thu, 05 Dec 2019 13:27:05: 15000000 INFO @ Thu, 05 Dec 2019 13:27:08: 9000000 INFO @ Thu, 05 Dec 2019 13:27:11: 15000000 INFO @ Thu, 05 Dec 2019 13:27:14: 16000000 INFO @ Thu, 05 Dec 2019 13:27:18: 10000000 INFO @ Thu, 05 Dec 2019 13:27:19: 16000000 INFO @ Thu, 05 Dec 2019 13:27:24: 17000000 INFO @ Thu, 05 Dec 2019 13:27:27: 17000000 INFO @ Thu, 05 Dec 2019 13:27:27: 11000000 INFO @ Thu, 05 Dec 2019 13:27:34: 18000000 INFO @ Thu, 05 Dec 2019 13:27:35: 18000000 INFO @ Thu, 05 Dec 2019 13:27:37: 12000000 INFO @ Thu, 05 Dec 2019 13:27:44: 19000000 INFO @ Thu, 05 Dec 2019 13:27:44: 19000000 INFO @ Thu, 05 Dec 2019 13:27:46: 13000000 INFO @ Thu, 05 Dec 2019 13:27:52: 20000000 INFO @ Thu, 05 Dec 2019 13:27:55: 20000000 INFO @ Thu, 05 Dec 2019 13:27:55: 14000000 INFO @ Thu, 05 Dec 2019 13:28:00: 21000000 INFO @ Thu, 05 Dec 2019 13:28:04: 21000000 INFO @ Thu, 05 Dec 2019 13:28:05: 15000000 INFO @ Thu, 05 Dec 2019 13:28:08: 22000000 INFO @ Thu, 05 Dec 2019 13:28:13: 22000000 INFO @ Thu, 05 Dec 2019 13:28:15: 16000000 INFO @ Thu, 05 Dec 2019 13:28:16: 23000000 INFO @ Thu, 05 Dec 2019 13:28:23: 23000000 INFO @ Thu, 05 Dec 2019 13:28:24: 24000000 INFO @ Thu, 05 Dec 2019 13:28:25: 17000000 INFO @ Thu, 05 Dec 2019 13:28:32: 25000000 INFO @ Thu, 05 Dec 2019 13:28:32: 24000000 INFO @ Thu, 05 Dec 2019 13:28:34: 18000000 INFO @ Thu, 05 Dec 2019 13:28:40: 26000000 INFO @ Thu, 05 Dec 2019 13:28:42: 25000000 INFO @ Thu, 05 Dec 2019 13:28:44: 19000000 INFO @ Thu, 05 Dec 2019 13:28:48: 27000000 INFO @ Thu, 05 Dec 2019 13:28:51: 26000000 INFO @ Thu, 05 Dec 2019 13:28:53: 20000000 INFO @ Thu, 05 Dec 2019 13:28:56: 28000000 INFO @ Thu, 05 Dec 2019 13:29:01: 27000000 INFO @ Thu, 05 Dec 2019 13:29:02: #1 tag size is determined as 79 bps INFO @ Thu, 05 Dec 2019 13:29:02: #1 tag size = 79 INFO @ Thu, 05 Dec 2019 13:29:02: #1 total tags in treatment: 13707148 INFO @ Thu, 05 Dec 2019 13:29:02: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:29:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:29:02: #1 tags after filtering in treatment: 11727447 INFO @ Thu, 05 Dec 2019 13:29:02: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 05 Dec 2019 13:29:02: #1 finished! INFO @ Thu, 05 Dec 2019 13:29:02: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:29:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:29:03: 21000000 INFO @ Thu, 05 Dec 2019 13:29:04: #2 number of paired peaks: 6748 INFO @ Thu, 05 Dec 2019 13:29:04: start model_add_line... INFO @ Thu, 05 Dec 2019 13:29:04: start X-correlation... INFO @ Thu, 05 Dec 2019 13:29:04: end of X-cor INFO @ Thu, 05 Dec 2019 13:29:04: #2 finished! INFO @ Thu, 05 Dec 2019 13:29:04: #2 predicted fragment length is 181 bps INFO @ Thu, 05 Dec 2019 13:29:04: #2 alternative fragment length(s) may be 4,181 bps INFO @ Thu, 05 Dec 2019 13:29:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.10_model.r INFO @ Thu, 05 Dec 2019 13:29:04: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:29:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:29:10: 28000000 INFO @ Thu, 05 Dec 2019 13:29:12: 22000000 INFO @ Thu, 05 Dec 2019 13:29:17: #1 tag size is determined as 79 bps INFO @ Thu, 05 Dec 2019 13:29:17: #1 tag size = 79 INFO @ Thu, 05 Dec 2019 13:29:17: #1 total tags in treatment: 13707148 INFO @ Thu, 05 Dec 2019 13:29:17: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:29:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:29:17: #1 tags after filtering in treatment: 11727447 INFO @ Thu, 05 Dec 2019 13:29:17: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 05 Dec 2019 13:29:17: #1 finished! INFO @ Thu, 05 Dec 2019 13:29:17: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:29:19: #2 number of paired peaks: 6748 INFO @ Thu, 05 Dec 2019 13:29:19: start model_add_line... INFO @ Thu, 05 Dec 2019 13:29:19: start X-correlation... INFO @ Thu, 05 Dec 2019 13:29:19: end of X-cor INFO @ Thu, 05 Dec 2019 13:29:19: #2 finished! INFO @ Thu, 05 Dec 2019 13:29:19: #2 predicted fragment length is 181 bps INFO @ Thu, 05 Dec 2019 13:29:19: #2 alternative fragment length(s) may be 4,181 bps INFO @ Thu, 05 Dec 2019 13:29:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.05_model.r INFO @ Thu, 05 Dec 2019 13:29:19: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:29:21: 23000000 INFO @ Thu, 05 Dec 2019 13:29:31: 24000000 INFO @ Thu, 05 Dec 2019 13:29:40: 25000000 INFO @ Thu, 05 Dec 2019 13:29:49: 26000000 INFO @ Thu, 05 Dec 2019 13:29:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:29:58: 27000000 INFO @ Thu, 05 Dec 2019 13:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.10_summits.bed INFO @ Thu, 05 Dec 2019 13:30:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1233 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:30:06: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:30:07: 28000000 INFO @ Thu, 05 Dec 2019 13:30:14: #1 tag size is determined as 79 bps INFO @ Thu, 05 Dec 2019 13:30:14: #1 tag size = 79 INFO @ Thu, 05 Dec 2019 13:30:14: #1 total tags in treatment: 13707148 INFO @ Thu, 05 Dec 2019 13:30:14: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:30:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:30:14: #1 tags after filtering in treatment: 11727447 INFO @ Thu, 05 Dec 2019 13:30:14: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 05 Dec 2019 13:30:14: #1 finished! INFO @ Thu, 05 Dec 2019 13:30:14: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:30:16: #2 number of paired peaks: 6748 INFO @ Thu, 05 Dec 2019 13:30:16: start model_add_line... INFO @ Thu, 05 Dec 2019 13:30:16: start X-correlation... INFO @ Thu, 05 Dec 2019 13:30:16: end of X-cor INFO @ Thu, 05 Dec 2019 13:30:16: #2 finished! INFO @ Thu, 05 Dec 2019 13:30:16: #2 predicted fragment length is 181 bps INFO @ Thu, 05 Dec 2019 13:30:16: #2 alternative fragment length(s) may be 4,181 bps INFO @ Thu, 05 Dec 2019 13:30:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.20_model.r INFO @ Thu, 05 Dec 2019 13:30:16: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:30:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.05_summits.bed INFO @ Thu, 05 Dec 2019 13:30:22: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2636 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:31:05: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:31:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:31:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:31:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5462365/SRX5462365.20_summits.bed INFO @ Thu, 05 Dec 2019 13:31:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。