Job ID = 1294999 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T02:13:15 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 ) 2019-06-03T02:13:15 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 ) 1900-01-00T00:00:00 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 ) 2019-06-03T02:13:15 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 ) 2019-06-03T02:13:15 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 ) 2019-06-03T02:13:15 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 : 23,815,084 reads read : 47,630,168 reads written : 47,630,168 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:37:11 23815084 reads; of these: 23815084 (100.00%) were paired; of these: 6233640 (26.18%) aligned concordantly 0 times 12817201 (53.82%) aligned concordantly exactly 1 time 4764243 (20.01%) aligned concordantly >1 times ---- 6233640 pairs aligned concordantly 0 times; of these: 243032 (3.90%) aligned discordantly 1 time ---- 5990608 pairs aligned 0 times concordantly or discordantly; of these: 11981216 mates make up the pairs; of these: 7435056 (62.06%) aligned 0 times 2908791 (24.28%) aligned exactly 1 time 1637369 (13.67%) aligned >1 times 84.39% overall alignment rate Time searching: 00:37:11 Overall time: 00:37:11 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 12 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] 2851304 / 17625114 = 0.1618 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 @ Mon, 03 Jun 2019 12:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.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 @ Mon, 03 Jun 2019 12:06:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:06:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.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 @ Mon, 03 Jun 2019 12:06:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:06:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.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 @ Mon, 03 Jun 2019 12:06:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:06:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:06:50: 1000000 INFO @ Mon, 03 Jun 2019 12:06:50: 1000000 INFO @ Mon, 03 Jun 2019 12:06:51: 1000000 INFO @ Mon, 03 Jun 2019 12:06:57: 2000000 INFO @ Mon, 03 Jun 2019 12:06:57: 2000000 INFO @ Mon, 03 Jun 2019 12:06:59: 2000000 INFO @ Mon, 03 Jun 2019 12:07:04: 3000000 INFO @ Mon, 03 Jun 2019 12:07:04: 3000000 INFO @ Mon, 03 Jun 2019 12:07:07: 3000000 INFO @ Mon, 03 Jun 2019 12:07:11: 4000000 INFO @ Mon, 03 Jun 2019 12:07:12: 4000000 INFO @ Mon, 03 Jun 2019 12:07:15: 4000000 INFO @ Mon, 03 Jun 2019 12:07:18: 5000000 INFO @ Mon, 03 Jun 2019 12:07:19: 5000000 INFO @ Mon, 03 Jun 2019 12:07:23: 5000000 INFO @ Mon, 03 Jun 2019 12:07:25: 6000000 INFO @ Mon, 03 Jun 2019 12:07:26: 6000000 INFO @ Mon, 03 Jun 2019 12:07:32: 6000000 INFO @ Mon, 03 Jun 2019 12:07:32: 7000000 INFO @ Mon, 03 Jun 2019 12:07:33: 7000000 INFO @ Mon, 03 Jun 2019 12:07:39: 8000000 INFO @ Mon, 03 Jun 2019 12:07:40: 7000000 INFO @ Mon, 03 Jun 2019 12:07:40: 8000000 INFO @ Mon, 03 Jun 2019 12:07:46: 9000000 INFO @ Mon, 03 Jun 2019 12:07:47: 9000000 INFO @ Mon, 03 Jun 2019 12:07:48: 8000000 INFO @ Mon, 03 Jun 2019 12:07:54: 10000000 INFO @ Mon, 03 Jun 2019 12:07:54: 10000000 INFO @ Mon, 03 Jun 2019 12:07:55: 9000000 INFO @ Mon, 03 Jun 2019 12:08:01: 11000000 INFO @ Mon, 03 Jun 2019 12:08:01: 11000000 INFO @ Mon, 03 Jun 2019 12:08:03: 10000000 INFO @ Mon, 03 Jun 2019 12:08:08: 12000000 INFO @ Mon, 03 Jun 2019 12:08:08: 12000000 INFO @ Mon, 03 Jun 2019 12:08:11: 11000000 INFO @ Mon, 03 Jun 2019 12:08:14: 13000000 INFO @ Mon, 03 Jun 2019 12:08:15: 13000000 INFO @ Mon, 03 Jun 2019 12:08:18: 12000000 INFO @ Mon, 03 Jun 2019 12:08:21: 14000000 INFO @ Mon, 03 Jun 2019 12:08:22: 14000000 INFO @ Mon, 03 Jun 2019 12:08:26: 13000000 INFO @ Mon, 03 Jun 2019 12:08:29: 15000000 INFO @ Mon, 03 Jun 2019 12:08:29: 15000000 INFO @ Mon, 03 Jun 2019 12:08:34: 14000000 INFO @ Mon, 03 Jun 2019 12:08:36: 16000000 INFO @ Mon, 03 Jun 2019 12:08:36: 16000000 INFO @ Mon, 03 Jun 2019 12:08:42: 15000000 INFO @ Mon, 03 Jun 2019 12:08:43: 17000000 INFO @ Mon, 03 Jun 2019 12:08:43: 17000000 INFO @ Mon, 03 Jun 2019 12:08:50: 18000000 INFO @ Mon, 03 Jun 2019 12:08:50: 16000000 INFO @ Mon, 03 Jun 2019 12:08:50: 18000000 INFO @ Mon, 03 Jun 2019 12:08:56: 19000000 INFO @ Mon, 03 Jun 2019 12:08:57: 19000000 INFO @ Mon, 03 Jun 2019 12:08:58: 17000000 INFO @ Mon, 03 Jun 2019 12:09:03: 20000000 INFO @ Mon, 03 Jun 2019 12:09:04: 20000000 INFO @ Mon, 03 Jun 2019 12:09:05: 18000000 INFO @ Mon, 03 Jun 2019 12:09:10: 21000000 INFO @ Mon, 03 Jun 2019 12:09:11: 21000000 INFO @ Mon, 03 Jun 2019 12:09:13: 19000000 INFO @ Mon, 03 Jun 2019 12:09:17: 22000000 INFO @ Mon, 03 Jun 2019 12:09:17: 22000000 INFO @ Mon, 03 Jun 2019 12:09:21: 20000000 INFO @ Mon, 03 Jun 2019 12:09:23: 23000000 INFO @ Mon, 03 Jun 2019 12:09:24: 23000000 INFO @ Mon, 03 Jun 2019 12:09:29: 21000000 INFO @ Mon, 03 Jun 2019 12:09:30: 24000000 INFO @ Mon, 03 Jun 2019 12:09:31: 24000000 INFO @ Mon, 03 Jun 2019 12:09:37: 22000000 INFO @ Mon, 03 Jun 2019 12:09:37: 25000000 INFO @ Mon, 03 Jun 2019 12:09:38: 25000000 INFO @ Mon, 03 Jun 2019 12:09:44: 23000000 INFO @ Mon, 03 Jun 2019 12:09:45: 26000000 INFO @ Mon, 03 Jun 2019 12:09:45: 26000000 INFO @ Mon, 03 Jun 2019 12:09:52: 27000000 INFO @ Mon, 03 Jun 2019 12:09:52: 27000000 INFO @ Mon, 03 Jun 2019 12:09:52: 24000000 INFO @ Mon, 03 Jun 2019 12:09:58: 28000000 INFO @ Mon, 03 Jun 2019 12:09:59: 28000000 INFO @ Mon, 03 Jun 2019 12:10:00: 25000000 INFO @ Mon, 03 Jun 2019 12:10:06: 29000000 INFO @ Mon, 03 Jun 2019 12:10:07: 29000000 INFO @ Mon, 03 Jun 2019 12:10:08: 26000000 INFO @ Mon, 03 Jun 2019 12:10:13: 30000000 INFO @ Mon, 03 Jun 2019 12:10:14: 30000000 INFO @ Mon, 03 Jun 2019 12:10:16: 27000000 INFO @ Mon, 03 Jun 2019 12:10:19: 31000000 INFO @ Mon, 03 Jun 2019 12:10:21: 31000000 INFO @ Mon, 03 Jun 2019 12:10:23: 28000000 INFO @ Mon, 03 Jun 2019 12:10:26: 32000000 INFO @ Mon, 03 Jun 2019 12:10:27: 32000000 INFO @ Mon, 03 Jun 2019 12:10:30: 29000000 INFO @ Mon, 03 Jun 2019 12:10:32: 33000000 INFO @ Mon, 03 Jun 2019 12:10:34: 33000000 INFO @ Mon, 03 Jun 2019 12:10:38: 30000000 INFO @ Mon, 03 Jun 2019 12:10:39: 34000000 INFO @ Mon, 03 Jun 2019 12:10:40: 34000000 INFO @ Mon, 03 Jun 2019 12:10:42: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:10:42: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:10:42: #1 total tags in treatment: 14734794 INFO @ Mon, 03 Jun 2019 12:10:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:10:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:10:42: #1 tags after filtering in treatment: 11862230 INFO @ Mon, 03 Jun 2019 12:10:42: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 12:10:42: #1 finished! INFO @ Mon, 03 Jun 2019 12:10:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:10:43: #2 number of paired peaks: 258 WARNING @ Mon, 03 Jun 2019 12:10:43: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Mon, 03 Jun 2019 12:10:43: start model_add_line... INFO @ Mon, 03 Jun 2019 12:10:43: start X-correlation... INFO @ Mon, 03 Jun 2019 12:10:43: end of X-cor INFO @ Mon, 03 Jun 2019 12:10:43: #2 finished! INFO @ Mon, 03 Jun 2019 12:10:43: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 12:10:43: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 03 Jun 2019 12:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.10_model.r INFO @ Mon, 03 Jun 2019 12:10:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:10:44: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:10:44: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:10:44: #1 total tags in treatment: 14734794 INFO @ Mon, 03 Jun 2019 12:10:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:10:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:10:44: #1 tags after filtering in treatment: 11862230 INFO @ Mon, 03 Jun 2019 12:10:44: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 12:10:44: #1 finished! INFO @ Mon, 03 Jun 2019 12:10:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:10:45: #2 number of paired peaks: 258 WARNING @ Mon, 03 Jun 2019 12:10:45: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Mon, 03 Jun 2019 12:10:45: start model_add_line... INFO @ Mon, 03 Jun 2019 12:10:45: 31000000 INFO @ Mon, 03 Jun 2019 12:10:45: start X-correlation... INFO @ Mon, 03 Jun 2019 12:10:45: end of X-cor INFO @ Mon, 03 Jun 2019 12:10:45: #2 finished! INFO @ Mon, 03 Jun 2019 12:10:45: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 12:10:45: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 03 Jun 2019 12:10:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.05_model.r INFO @ Mon, 03 Jun 2019 12:10:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:10:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:10:52: 32000000 INFO @ Mon, 03 Jun 2019 12:11:00: 33000000 INFO @ Mon, 03 Jun 2019 12:11:07: 34000000 INFO @ Mon, 03 Jun 2019 12:11:11: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:11:11: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:11:11: #1 total tags in treatment: 14734794 INFO @ Mon, 03 Jun 2019 12:11:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:11:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 12:11:11: #1 tags after filtering in treatment: 11862230 INFO @ Mon, 03 Jun 2019 12:11:11: #1 Redundant rate of treatment: 0.19 INFO @ Mon, 03 Jun 2019 12:11:11: #1 finished! INFO @ Mon, 03 Jun 2019 12:11:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:11:12: #2 number of paired peaks: 258 WARNING @ Mon, 03 Jun 2019 12:11:12: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Mon, 03 Jun 2019 12:11:12: start model_add_line... INFO @ Mon, 03 Jun 2019 12:11:12: start X-correlation... INFO @ Mon, 03 Jun 2019 12:11:12: end of X-cor INFO @ Mon, 03 Jun 2019 12:11:12: #2 finished! INFO @ Mon, 03 Jun 2019 12:11:12: #2 predicted fragment length is 99 bps INFO @ Mon, 03 Jun 2019 12:11:12: #2 alternative fragment length(s) may be 99 bps INFO @ Mon, 03 Jun 2019 12:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.20_model.r INFO @ Mon, 03 Jun 2019 12:11:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:11:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:11:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:11:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:11:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:11:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.10_summits.bed INFO @ Mon, 03 Jun 2019 12:11:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1374 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:11:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:11:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:11:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.05_summits.bed INFO @ Mon, 03 Jun 2019 12:11:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2480 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:11:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:12:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:12:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300933/SRX300933.20_summits.bed INFO @ Mon, 03 Jun 2019 12:12:03: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (700 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。