Job ID = 4178445 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-05T03:31:03 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 ) 2019-12-05T03:32:28 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 ) 2019-12-05T03:44:08 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 : 19,082,257 reads read : 38,164,514 reads written : 38,164,514 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: 00:00:01 Multiseed full-index search: 01:20:29 19082257 reads; of these: 19082257 (100.00%) were paired; of these: 4449611 (23.32%) aligned concordantly 0 times 10912836 (57.19%) aligned concordantly exactly 1 time 3719810 (19.49%) aligned concordantly >1 times ---- 4449611 pairs aligned concordantly 0 times; of these: 2079438 (46.73%) aligned discordantly 1 time ---- 2370173 pairs aligned 0 times concordantly or discordantly; of these: 4740346 mates make up the pairs; of these: 2849933 (60.12%) aligned 0 times 721270 (15.22%) aligned exactly 1 time 1169143 (24.66%) aligned >1 times 92.53% overall alignment rate Time searching: 01:20:30 Overall time: 01:20:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 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] 989925 / 16661912 = 0.0594 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 14:36:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.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 14:36:23: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:36:23: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:36:35: 1000000 INFO @ Thu, 05 Dec 2019 14:36:46: 2000000 INFO @ Thu, 05 Dec 2019 14:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.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 14:36:51: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:36:51: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:36:58: 3000000 INFO @ Thu, 05 Dec 2019 14:37:03: 1000000 INFO @ Thu, 05 Dec 2019 14:37:12: 4000000 INFO @ Thu, 05 Dec 2019 14:37:17: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 14:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.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 14:37:21: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:37:21: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:37:26: 5000000 INFO @ Thu, 05 Dec 2019 14:37:31: 3000000 INFO @ Thu, 05 Dec 2019 14:37:33: 1000000 INFO @ Thu, 05 Dec 2019 14:37:42: 6000000 INFO @ Thu, 05 Dec 2019 14:37:52: 4000000 INFO @ Thu, 05 Dec 2019 14:37:55: 2000000 INFO @ Thu, 05 Dec 2019 14:38:02: 7000000 INFO @ Thu, 05 Dec 2019 14:38:10: 3000000 INFO @ Thu, 05 Dec 2019 14:38:10: 5000000 INFO @ Thu, 05 Dec 2019 14:38:16: 8000000 INFO @ Thu, 05 Dec 2019 14:38:21: 4000000 INFO @ Thu, 05 Dec 2019 14:38:23: 6000000 INFO @ Thu, 05 Dec 2019 14:38:28: 9000000 INFO @ Thu, 05 Dec 2019 14:38:33: 5000000 INFO @ Thu, 05 Dec 2019 14:38:36: 7000000 INFO @ Thu, 05 Dec 2019 14:38:42: 10000000 INFO @ Thu, 05 Dec 2019 14:38:44: 6000000 INFO @ Thu, 05 Dec 2019 14:38:49: 8000000 INFO @ Thu, 05 Dec 2019 14:38:55: 11000000 INFO @ Thu, 05 Dec 2019 14:38:56: 7000000 INFO @ Thu, 05 Dec 2019 14:39:02: 9000000 INFO @ Thu, 05 Dec 2019 14:39:07: 8000000 INFO @ Thu, 05 Dec 2019 14:39:08: 12000000 INFO @ Thu, 05 Dec 2019 14:39:16: 10000000 INFO @ Thu, 05 Dec 2019 14:39:18: 9000000 INFO @ Thu, 05 Dec 2019 14:39:21: 13000000 INFO @ Thu, 05 Dec 2019 14:39:30: 10000000 INFO @ Thu, 05 Dec 2019 14:39:30: 11000000 INFO @ Thu, 05 Dec 2019 14:39:34: 14000000 INFO @ Thu, 05 Dec 2019 14:39:41: 11000000 INFO @ Thu, 05 Dec 2019 14:39:44: 12000000 INFO @ Thu, 05 Dec 2019 14:39:47: 15000000 INFO @ Thu, 05 Dec 2019 14:39:53: 12000000 INFO @ Thu, 05 Dec 2019 14:39:58: 13000000 INFO @ Thu, 05 Dec 2019 14:40:00: 16000000 INFO @ Thu, 05 Dec 2019 14:40:03: 13000000 INFO @ Thu, 05 Dec 2019 14:40:13: 14000000 INFO @ Thu, 05 Dec 2019 14:40:15: 17000000 INFO @ Thu, 05 Dec 2019 14:40:16: 14000000 INFO @ Thu, 05 Dec 2019 14:40:26: 15000000 INFO @ Thu, 05 Dec 2019 14:40:27: 15000000 INFO @ Thu, 05 Dec 2019 14:40:28: 18000000 INFO @ Thu, 05 Dec 2019 14:40:38: 16000000 INFO @ Thu, 05 Dec 2019 14:40:39: 16000000 INFO @ Thu, 05 Dec 2019 14:40:41: 19000000 INFO @ Thu, 05 Dec 2019 14:40:50: 17000000 INFO @ Thu, 05 Dec 2019 14:40:51: 17000000 INFO @ Thu, 05 Dec 2019 14:40:54: 20000000 INFO @ Thu, 05 Dec 2019 14:41:02: 18000000 INFO @ Thu, 05 Dec 2019 14:41:03: 18000000 INFO @ Thu, 05 Dec 2019 14:41:07: 21000000 INFO @ Thu, 05 Dec 2019 14:41:14: 19000000 INFO @ Thu, 05 Dec 2019 14:41:15: 19000000 INFO @ Thu, 05 Dec 2019 14:41:20: 22000000 INFO @ Thu, 05 Dec 2019 14:41:27: 20000000 INFO @ Thu, 05 Dec 2019 14:41:28: 20000000 INFO @ Thu, 05 Dec 2019 14:41:33: 23000000 INFO @ Thu, 05 Dec 2019 14:41:38: 21000000 INFO @ Thu, 05 Dec 2019 14:41:40: 21000000 INFO @ Thu, 05 Dec 2019 14:41:46: 24000000 INFO @ Thu, 05 Dec 2019 14:41:49: 22000000 INFO @ Thu, 05 Dec 2019 14:41:55: 22000000 INFO @ Thu, 05 Dec 2019 14:41:59: 25000000 INFO @ Thu, 05 Dec 2019 14:42:00: 23000000 INFO @ Thu, 05 Dec 2019 14:42:10: 23000000 INFO @ Thu, 05 Dec 2019 14:42:11: 24000000 INFO @ Thu, 05 Dec 2019 14:42:12: 26000000 INFO @ Thu, 05 Dec 2019 14:42:24: 25000000 INFO @ Thu, 05 Dec 2019 14:42:24: 24000000 INFO @ Thu, 05 Dec 2019 14:42:26: 27000000 INFO @ Thu, 05 Dec 2019 14:42:36: 26000000 INFO @ Thu, 05 Dec 2019 14:42:38: 25000000 INFO @ Thu, 05 Dec 2019 14:42:40: 28000000 INFO @ Thu, 05 Dec 2019 14:42:47: 27000000 INFO @ Thu, 05 Dec 2019 14:42:51: 26000000 INFO @ Thu, 05 Dec 2019 14:42:53: 29000000 INFO @ Thu, 05 Dec 2019 14:42:59: 28000000 INFO @ Thu, 05 Dec 2019 14:43:04: 27000000 INFO @ Thu, 05 Dec 2019 14:43:06: 30000000 INFO @ Thu, 05 Dec 2019 14:43:10: 29000000 INFO @ Thu, 05 Dec 2019 14:43:16: 28000000 INFO @ Thu, 05 Dec 2019 14:43:20: 31000000 INFO @ Thu, 05 Dec 2019 14:43:22: 30000000 INFO @ Thu, 05 Dec 2019 14:43:29: 29000000 INFO @ Thu, 05 Dec 2019 14:43:33: 32000000 INFO @ Thu, 05 Dec 2019 14:43:34: 31000000 INFO @ Thu, 05 Dec 2019 14:43:43: 30000000 INFO @ Thu, 05 Dec 2019 14:43:46: 32000000 INFO @ Thu, 05 Dec 2019 14:43:47: 33000000 INFO @ Thu, 05 Dec 2019 14:43:51: #1 tag size is determined as 98 bps INFO @ Thu, 05 Dec 2019 14:43:51: #1 tag size = 98 INFO @ Thu, 05 Dec 2019 14:43:51: #1 total tags in treatment: 13789569 INFO @ Thu, 05 Dec 2019 14:43:51: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:43:51: #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 14:43:51: #1 tags after filtering in treatment: 12843916 INFO @ Thu, 05 Dec 2019 14:43:51: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 14:43:51: #1 finished! INFO @ Thu, 05 Dec 2019 14:43:51: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:43:53: #2 number of paired peaks: 457 WARNING @ Thu, 05 Dec 2019 14:43:53: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Thu, 05 Dec 2019 14:43:53: start model_add_line... INFO @ Thu, 05 Dec 2019 14:43:53: start X-correlation... INFO @ Thu, 05 Dec 2019 14:43:53: end of X-cor INFO @ Thu, 05 Dec 2019 14:43:53: #2 finished! INFO @ Thu, 05 Dec 2019 14:43:53: #2 predicted fragment length is 312 bps INFO @ Thu, 05 Dec 2019 14:43:53: #2 alternative fragment length(s) may be 312 bps INFO @ Thu, 05 Dec 2019 14:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.05_model.r INFO @ Thu, 05 Dec 2019 14:43:53: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:43:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:43:55: 31000000 INFO @ Thu, 05 Dec 2019 14:43:57: 33000000 INFO @ Thu, 05 Dec 2019 14:44:01: #1 tag size is determined as 98 bps INFO @ Thu, 05 Dec 2019 14:44:01: #1 tag size = 98 INFO @ Thu, 05 Dec 2019 14:44:01: #1 total tags in treatment: 13789569 INFO @ Thu, 05 Dec 2019 14:44:01: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:44:01: #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 14:44:02: #1 tags after filtering in treatment: 12843916 INFO @ Thu, 05 Dec 2019 14:44:02: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 14:44:02: #1 finished! INFO @ Thu, 05 Dec 2019 14:44:02: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:44:03: #2 number of paired peaks: 457 WARNING @ Thu, 05 Dec 2019 14:44:03: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Thu, 05 Dec 2019 14:44:03: start model_add_line... INFO @ Thu, 05 Dec 2019 14:44:03: start X-correlation... INFO @ Thu, 05 Dec 2019 14:44:03: end of X-cor INFO @ Thu, 05 Dec 2019 14:44:03: #2 finished! INFO @ Thu, 05 Dec 2019 14:44:03: #2 predicted fragment length is 312 bps INFO @ Thu, 05 Dec 2019 14:44:03: #2 alternative fragment length(s) may be 312 bps INFO @ Thu, 05 Dec 2019 14:44:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.20_model.r INFO @ Thu, 05 Dec 2019 14:44:03: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:44:07: 32000000 INFO @ Thu, 05 Dec 2019 14:44:18: 33000000 INFO @ Thu, 05 Dec 2019 14:44:22: #1 tag size is determined as 98 bps INFO @ Thu, 05 Dec 2019 14:44:22: #1 tag size = 98 INFO @ Thu, 05 Dec 2019 14:44:22: #1 total tags in treatment: 13789569 INFO @ Thu, 05 Dec 2019 14:44:22: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:44:22: #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 14:44:23: #1 tags after filtering in treatment: 12843916 INFO @ Thu, 05 Dec 2019 14:44:23: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 14:44:23: #1 finished! INFO @ Thu, 05 Dec 2019 14:44:23: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:44:24: #2 number of paired peaks: 457 WARNING @ Thu, 05 Dec 2019 14:44:24: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Thu, 05 Dec 2019 14:44:24: start model_add_line... INFO @ Thu, 05 Dec 2019 14:44:24: start X-correlation... INFO @ Thu, 05 Dec 2019 14:44:24: end of X-cor INFO @ Thu, 05 Dec 2019 14:44:24: #2 finished! INFO @ Thu, 05 Dec 2019 14:44:24: #2 predicted fragment length is 312 bps INFO @ Thu, 05 Dec 2019 14:44:24: #2 alternative fragment length(s) may be 312 bps INFO @ Thu, 05 Dec 2019 14:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.10_model.r INFO @ Thu, 05 Dec 2019 14:44:24: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:44:33: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:44:41: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:44:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.05_peaks.xls INFO @ Thu, 05 Dec 2019 14:44:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:44:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.05_summits.bed INFO @ Thu, 05 Dec 2019 14:44:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2781 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.20_peaks.xls INFO @ Thu, 05 Dec 2019 14:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.20_summits.bed INFO @ Thu, 05 Dec 2019 14:45:00: Done! pass1 - making usageList (12 chroms): 4 millis pass2 - checking and writing primary data (1013 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:45:03: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.10_peaks.xls INFO @ Thu, 05 Dec 2019 14:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117269/SRX4117269.10_summits.bed INFO @ Thu, 05 Dec 2019 14:45:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1636 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。