Job ID = 2640422 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:39:35 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 ) 2019-08-24T07:39:35 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 ) 2019-08-24T07:40:54 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 ) 2019-08-24T07:43:28 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 ) 2019-08-24T07:43:28 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 ) 2019-08-24T07:44:11 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 ) 2019-08-24T07:47:57 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 ) 2019-08-24T07:47:57 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 ) 2019-08-24T07:49:05 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 ) 2019-08-24T07:53:48 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 : 48,969,460 reads read : 48,969,460 reads written : 48,969,460 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:22:33 48969460 reads; of these: 48969460 (100.00%) were unpaired; of these: 22510701 (45.97%) aligned 0 times 17023324 (34.76%) aligned exactly 1 time 9435435 (19.27%) aligned >1 times 54.03% overall alignment rate Time searching: 00:22:36 Overall time: 00:22:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1469995 / 26458759 = 0.0556 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:27:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:27:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:27:47: 1000000 INFO @ Sat, 24 Aug 2019 17:27:55: 2000000 INFO @ Sat, 24 Aug 2019 17:28:04: 3000000 INFO @ Sat, 24 Aug 2019 17:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:28:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:28:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:28:13: 4000000 INFO @ Sat, 24 Aug 2019 17:28:17: 1000000 INFO @ Sat, 24 Aug 2019 17:28:22: 5000000 INFO @ Sat, 24 Aug 2019 17:28:26: 2000000 INFO @ Sat, 24 Aug 2019 17:28:31: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:28:35: 3000000 INFO @ Sat, 24 Aug 2019 17:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:28:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:28:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:28:40: 7000000 INFO @ Sat, 24 Aug 2019 17:28:45: 4000000 INFO @ Sat, 24 Aug 2019 17:28:45: 1000000 INFO @ Sat, 24 Aug 2019 17:28:50: 8000000 INFO @ Sat, 24 Aug 2019 17:28:53: 2000000 INFO @ Sat, 24 Aug 2019 17:28:54: 5000000 INFO @ Sat, 24 Aug 2019 17:28:59: 9000000 INFO @ Sat, 24 Aug 2019 17:29:00: 3000000 INFO @ Sat, 24 Aug 2019 17:29:03: 6000000 INFO @ Sat, 24 Aug 2019 17:29:08: 4000000 INFO @ Sat, 24 Aug 2019 17:29:08: 10000000 INFO @ Sat, 24 Aug 2019 17:29:12: 7000000 INFO @ Sat, 24 Aug 2019 17:29:15: 5000000 INFO @ Sat, 24 Aug 2019 17:29:18: 11000000 INFO @ Sat, 24 Aug 2019 17:29:22: 8000000 INFO @ Sat, 24 Aug 2019 17:29:23: 6000000 INFO @ Sat, 24 Aug 2019 17:29:27: 12000000 INFO @ Sat, 24 Aug 2019 17:29:31: 7000000 INFO @ Sat, 24 Aug 2019 17:29:31: 9000000 INFO @ Sat, 24 Aug 2019 17:29:36: 13000000 INFO @ Sat, 24 Aug 2019 17:29:38: 8000000 INFO @ Sat, 24 Aug 2019 17:29:40: 10000000 INFO @ Sat, 24 Aug 2019 17:29:46: 9000000 INFO @ Sat, 24 Aug 2019 17:29:46: 14000000 INFO @ Sat, 24 Aug 2019 17:29:50: 11000000 INFO @ Sat, 24 Aug 2019 17:29:53: 10000000 INFO @ Sat, 24 Aug 2019 17:29:55: 15000000 INFO @ Sat, 24 Aug 2019 17:29:59: 12000000 INFO @ Sat, 24 Aug 2019 17:30:01: 11000000 INFO @ Sat, 24 Aug 2019 17:30:04: 16000000 INFO @ Sat, 24 Aug 2019 17:30:08: 13000000 INFO @ Sat, 24 Aug 2019 17:30:08: 12000000 INFO @ Sat, 24 Aug 2019 17:30:13: 17000000 INFO @ Sat, 24 Aug 2019 17:30:16: 13000000 INFO @ Sat, 24 Aug 2019 17:30:17: 14000000 INFO @ Sat, 24 Aug 2019 17:30:23: 18000000 INFO @ Sat, 24 Aug 2019 17:30:23: 14000000 INFO @ Sat, 24 Aug 2019 17:30:26: 15000000 INFO @ Sat, 24 Aug 2019 17:30:31: 15000000 INFO @ Sat, 24 Aug 2019 17:30:32: 19000000 INFO @ Sat, 24 Aug 2019 17:30:36: 16000000 INFO @ Sat, 24 Aug 2019 17:30:38: 16000000 INFO @ Sat, 24 Aug 2019 17:30:41: 20000000 INFO @ Sat, 24 Aug 2019 17:30:45: 17000000 INFO @ Sat, 24 Aug 2019 17:30:45: 17000000 INFO @ Sat, 24 Aug 2019 17:30:50: 21000000 INFO @ Sat, 24 Aug 2019 17:30:53: 18000000 INFO @ Sat, 24 Aug 2019 17:30:54: 18000000 INFO @ Sat, 24 Aug 2019 17:30:59: 22000000 INFO @ Sat, 24 Aug 2019 17:31:01: 19000000 INFO @ Sat, 24 Aug 2019 17:31:03: 19000000 INFO @ Sat, 24 Aug 2019 17:31:08: 20000000 INFO @ Sat, 24 Aug 2019 17:31:09: 23000000 INFO @ Sat, 24 Aug 2019 17:31:12: 20000000 INFO @ Sat, 24 Aug 2019 17:31:15: 21000000 INFO @ Sat, 24 Aug 2019 17:31:18: 24000000 INFO @ Sat, 24 Aug 2019 17:31:21: 21000000 INFO @ Sat, 24 Aug 2019 17:31:23: 22000000 INFO @ Sat, 24 Aug 2019 17:31:27: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:31:27: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:31:27: #1 total tags in treatment: 24988764 INFO @ Sat, 24 Aug 2019 17:31:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:31:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:31:28: #1 tags after filtering in treatment: 24988675 INFO @ Sat, 24 Aug 2019 17:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:31:28: #1 finished! INFO @ Sat, 24 Aug 2019 17:31:28: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:31:30: 22000000 INFO @ Sat, 24 Aug 2019 17:31:30: 23000000 INFO @ Sat, 24 Aug 2019 17:31:31: #2 number of paired peaks: 7302 INFO @ Sat, 24 Aug 2019 17:31:31: start model_add_line... INFO @ Sat, 24 Aug 2019 17:31:31: start X-correlation... INFO @ Sat, 24 Aug 2019 17:31:31: end of X-cor INFO @ Sat, 24 Aug 2019 17:31:31: #2 finished! INFO @ Sat, 24 Aug 2019 17:31:31: #2 predicted fragment length is 41 bps INFO @ Sat, 24 Aug 2019 17:31:31: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 24 Aug 2019 17:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.05_model.r WARNING @ Sat, 24 Aug 2019 17:31:31: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:31:31: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 24 Aug 2019 17:31:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:31:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:31:38: 24000000 INFO @ Sat, 24 Aug 2019 17:31:39: 23000000 INFO @ Sat, 24 Aug 2019 17:31:46: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:31:46: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:31:46: #1 total tags in treatment: 24988764 INFO @ Sat, 24 Aug 2019 17:31:46: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:31:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:31:46: #1 tags after filtering in treatment: 24988675 INFO @ Sat, 24 Aug 2019 17:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:31:46: #1 finished! INFO @ Sat, 24 Aug 2019 17:31:46: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:31:48: 24000000 INFO @ Sat, 24 Aug 2019 17:31:49: #2 number of paired peaks: 7302 INFO @ Sat, 24 Aug 2019 17:31:49: start model_add_line... INFO @ Sat, 24 Aug 2019 17:31:50: start X-correlation... INFO @ Sat, 24 Aug 2019 17:31:50: end of X-cor INFO @ Sat, 24 Aug 2019 17:31:50: #2 finished! INFO @ Sat, 24 Aug 2019 17:31:50: #2 predicted fragment length is 41 bps INFO @ Sat, 24 Aug 2019 17:31:50: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 24 Aug 2019 17:31:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.20_model.r WARNING @ Sat, 24 Aug 2019 17:31:50: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:31:50: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 24 Aug 2019 17:31:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:31:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:31:56: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:31:56: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:31:56: #1 total tags in treatment: 24988764 INFO @ Sat, 24 Aug 2019 17:31:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:31:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:31:57: #1 tags after filtering in treatment: 24988675 INFO @ Sat, 24 Aug 2019 17:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:31:57: #1 finished! INFO @ Sat, 24 Aug 2019 17:31:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:32:00: #2 number of paired peaks: 7302 INFO @ Sat, 24 Aug 2019 17:32:00: start model_add_line... INFO @ Sat, 24 Aug 2019 17:32:00: start X-correlation... INFO @ Sat, 24 Aug 2019 17:32:00: end of X-cor INFO @ Sat, 24 Aug 2019 17:32:00: #2 finished! INFO @ Sat, 24 Aug 2019 17:32:00: #2 predicted fragment length is 41 bps INFO @ Sat, 24 Aug 2019 17:32:00: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 24 Aug 2019 17:32:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.10_model.r WARNING @ Sat, 24 Aug 2019 17:32:00: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:32:00: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 24 Aug 2019 17:32:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:32:00: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:32:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:32:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:33:08: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:33:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:33:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.05_summits.bed INFO @ Sat, 24 Aug 2019 17:33:28: Done! pass1 - making usageList (87 chroms): 4 millis pass2 - checking and writing primary data (6320 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.20_summits.bed INFO @ Sat, 24 Aug 2019 17:33:47: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1034 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208971/SRX208971.10_summits.bed INFO @ Sat, 24 Aug 2019 17:33:56: Done! pass1 - making usageList (61 chroms): 3 millis pass2 - checking and writing primary data (2661 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。