Job ID = 3785910 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:39:18 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 ) 2019-11-01T05:39:18 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 ) 2019-11-01T05:39:18 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 ) 2019-11-01T05:39:36 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 ) 2019-11-01T05:39:36 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 ) 2019-11-01T05:39:47 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 ) 2019-11-01T05:39:56 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 ) 2019-11-01T05:40:31 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 ) 2019-11-01T05:43:18 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-11-01T05:43:21 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 ) 2019-11-01T05:43:32 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 ) 2019-11-01T05:44:12 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-11-01T05:44:44 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 ) 2019-11-01T05:45:15 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 ) 2019-11-01T05:45:15 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 ) 2019-11-01T05:45:55 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 ) 2019-11-01T05:46:11 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-11-01T05:46:27 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 ) 2019-11-01T05:46:37 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 ) 2019-11-01T05:46:45 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 ) 2019-11-01T05:46:54 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 ) 2019-11-01T05:48:25 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 ) 2019-11-01T05:48:25 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 ) 2019-11-01T05:48:30 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 ) 2019-11-01T05:48:43 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 ) 2019-11-01T05:49:46 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 ) 2019-11-01T05:49:57 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 ) 2019-11-01T05:50:19 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 ) 2019-11-01T05:51:21 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 ) 2019-11-01T05:52:33 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 ) 2019-11-01T05:53:11 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 ) 2019-11-01T05:53:13 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 ) 2019-11-01T05:53:15 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 ) 2019-11-01T05:53:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-11-01T05:53:55 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 ) 2019-11-01T05:54:51 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 ) 2019-11-01T05:55:25 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 ) 2019-11-01T05:55:43 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 ) 2019-11-01T05:55:58 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 ) 2019-11-01T05:57:35 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-11-01T05:57:44 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 ) 2019-11-01T05:59:02 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 ) 2019-11-01T06:00:04 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 ) 2019-11-01T06:00:35 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 ) 2019-11-01T06:05:30 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 : 47,372,438 reads read : 94,744,876 reads written : 47,372,438 reads 0-length : 47,372,438 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: 00:06:51 47372438 reads; of these: 47372438 (100.00%) were unpaired; of these: 39008840 (82.35%) aligned 0 times 7186039 (15.17%) aligned exactly 1 time 1177559 (2.49%) aligned >1 times 17.65% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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_rmdupse_core] 1158877 / 8363598 = 0.1386 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 15:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.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 @ Fri, 01 Nov 2019 15:15:39: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:15:39: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:15:47: 1000000 INFO @ Fri, 01 Nov 2019 15:15:55: 2000000 INFO @ Fri, 01 Nov 2019 15:16:03: 3000000 INFO @ Fri, 01 Nov 2019 15:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.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 @ Fri, 01 Nov 2019 15:16:08: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:16:08: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:16:10: 4000000 INFO @ Fri, 01 Nov 2019 15:16:18: 5000000 INFO @ Fri, 01 Nov 2019 15:16:19: 1000000 INFO @ Fri, 01 Nov 2019 15:16:25: 6000000 INFO @ Fri, 01 Nov 2019 15:16:30: 2000000 INFO @ Fri, 01 Nov 2019 15:16:33: 7000000 INFO @ Fri, 01 Nov 2019 15:16:34: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:16:34: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:16:34: #1 total tags in treatment: 7204721 INFO @ Fri, 01 Nov 2019 15:16:34: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:16:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 15:16:34: #1 tags after filtering in treatment: 7204721 INFO @ Fri, 01 Nov 2019 15:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:16:34: #1 finished! INFO @ Fri, 01 Nov 2019 15:16:34: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:16:34: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... INFO @ Fri, 01 Nov 2019 15:16:36: #2 number of paired peaks: 11260 INFO @ Fri, 01 Nov 2019 15:16:36: start model_add_line... INFO @ Fri, 01 Nov 2019 15:16:36: start X-correlation... INFO @ Fri, 01 Nov 2019 15:16:36: end of X-cor INFO @ Fri, 01 Nov 2019 15:16:36: #2 finished! INFO @ Fri, 01 Nov 2019 15:16:36: #2 predicted fragment length is 189 bps INFO @ Fri, 01 Nov 2019 15:16:36: #2 alternative fragment length(s) may be 4,189 bps INFO @ Fri, 01 Nov 2019 15:16:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.05_model.r INFO @ Fri, 01 Nov 2019 15:16:36: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:16:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.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 @ Fri, 01 Nov 2019 15:16:38: #1 read tag files... INFO @ Fri, 01 Nov 2019 15:16:38: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 15:16:41: 3000000 INFO @ Fri, 01 Nov 2019 15:16:46: 1000000 INFO @ Fri, 01 Nov 2019 15:16:51: 4000000 INFO @ Fri, 01 Nov 2019 15:16:54: 2000000 INFO @ Fri, 01 Nov 2019 15:16:59: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:17:02: 3000000 INFO @ Fri, 01 Nov 2019 15:17:02: 5000000 INFO @ Fri, 01 Nov 2019 15:17:09: 4000000 INFO @ Fri, 01 Nov 2019 15:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.05_peaks.xls INFO @ Fri, 01 Nov 2019 15:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.05_summits.bed INFO @ Fri, 01 Nov 2019 15:17:11: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7984 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 15:17:12: 6000000 INFO @ Fri, 01 Nov 2019 15:17:17: 5000000 INFO @ Fri, 01 Nov 2019 15:17:23: 7000000 INFO @ Fri, 01 Nov 2019 15:17:24: 6000000 INFO @ Fri, 01 Nov 2019 15:17:25: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:17:25: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:17:25: #1 total tags in treatment: 7204721 INFO @ Fri, 01 Nov 2019 15:17:25: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:17:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 15:17:25: #1 tags after filtering in treatment: 7204721 INFO @ Fri, 01 Nov 2019 15:17:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:17:25: #1 finished! INFO @ Fri, 01 Nov 2019 15:17:25: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:17:27: #2 number of paired peaks: 11260 INFO @ Fri, 01 Nov 2019 15:17:27: start model_add_line... INFO @ Fri, 01 Nov 2019 15:17:27: start X-correlation... INFO @ Fri, 01 Nov 2019 15:17:27: end of X-cor INFO @ Fri, 01 Nov 2019 15:17:27: #2 finished! INFO @ Fri, 01 Nov 2019 15:17:27: #2 predicted fragment length is 189 bps INFO @ Fri, 01 Nov 2019 15:17:27: #2 alternative fragment length(s) may be 4,189 bps INFO @ Fri, 01 Nov 2019 15:17:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.10_model.r INFO @ Fri, 01 Nov 2019 15:17:27: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:17:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:17:32: 7000000 INFO @ Fri, 01 Nov 2019 15:17:33: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 15:17:33: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 15:17:33: #1 total tags in treatment: 7204721 INFO @ Fri, 01 Nov 2019 15:17:33: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 15:17:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 15:17:33: #1 tags after filtering in treatment: 7204721 INFO @ Fri, 01 Nov 2019 15:17:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 15:17:33: #1 finished! INFO @ Fri, 01 Nov 2019 15:17:33: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 15:17:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 15:17:35: #2 number of paired peaks: 11260 INFO @ Fri, 01 Nov 2019 15:17:35: start model_add_line... INFO @ Fri, 01 Nov 2019 15:17:35: start X-correlation... INFO @ Fri, 01 Nov 2019 15:17:35: end of X-cor INFO @ Fri, 01 Nov 2019 15:17:35: #2 finished! INFO @ Fri, 01 Nov 2019 15:17:35: #2 predicted fragment length is 189 bps INFO @ Fri, 01 Nov 2019 15:17:35: #2 alternative fragment length(s) may be 4,189 bps INFO @ Fri, 01 Nov 2019 15:17:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.20_model.r INFO @ Fri, 01 Nov 2019 15:17:35: #3 Call peaks... INFO @ Fri, 01 Nov 2019 15:17:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 15:17:50: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:17:58: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 15:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.10_peaks.xls INFO @ Fri, 01 Nov 2019 15:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.10_summits.bed INFO @ Fri, 01 Nov 2019 15:18:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4038 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 15:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.20_peaks.xls INFO @ Fri, 01 Nov 2019 15:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 15:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5850003/SRX5850003.20_summits.bed INFO @ Fri, 01 Nov 2019 15:18:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1300 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。