Job ID = 3785863 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:35:40 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 ) 2019-11-01T05:35:40 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 ) 2019-11-01T05:36:06 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 ) 2019-11-01T05:36:12 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 ) 2019-11-01T05:36:40 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 ) 2019-11-01T05:37:55 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:39:46 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 ) 2019-11-01T05:39:56 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 ) 2019-11-01T05:40:06 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 ) 2019-11-01T05:40:42 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 ) 2019-11-01T05:41:13 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 ) 2019-11-01T05:41:35 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 ) 2019-11-01T05:46:12 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 : 9,923,737 reads read : 9,923,737 reads written : 9,923,737 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: 00:04:04 9923737 reads; of these: 9923737 (100.00%) were unpaired; of these: 489490 (4.93%) aligned 0 times 5939782 (59.85%) aligned exactly 1 time 3494465 (35.21%) aligned >1 times 95.07% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 491239 / 9434247 = 0.0521 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.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 14:53:56: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:53:56: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:54:02: 1000000 INFO @ Fri, 01 Nov 2019 14:54:09: 2000000 INFO @ Fri, 01 Nov 2019 14:54:15: 3000000 INFO @ Fri, 01 Nov 2019 14:54:22: 4000000 INFO @ Fri, 01 Nov 2019 14:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.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 14:54:24: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:54:24: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:54:29: 5000000 INFO @ Fri, 01 Nov 2019 14:54:31: 1000000 INFO @ Fri, 01 Nov 2019 14:54:35: 6000000 INFO @ Fri, 01 Nov 2019 14:54:38: 2000000 INFO @ Fri, 01 Nov 2019 14:54:42: 7000000 INFO @ Fri, 01 Nov 2019 14:54:44: 3000000 INFO @ Fri, 01 Nov 2019 14:54:49: 8000000 INFO @ Fri, 01 Nov 2019 14:54:51: 4000000 BedGraph に変換中... INFO @ Fri, 01 Nov 2019 14:54:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.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 14:54:54: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:54:54: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:54:55: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:54:55: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:54:55: #1 total tags in treatment: 8943008 INFO @ Fri, 01 Nov 2019 14:54:55: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:54:55: #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 14:54:55: #1 tags after filtering in treatment: 8943008 INFO @ Fri, 01 Nov 2019 14:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:54:55: #1 finished! INFO @ Fri, 01 Nov 2019 14:54:55: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:54:56: #2 number of paired peaks: 1095 INFO @ Fri, 01 Nov 2019 14:54:56: start model_add_line... INFO @ Fri, 01 Nov 2019 14:54:56: start X-correlation... INFO @ Fri, 01 Nov 2019 14:54:57: end of X-cor INFO @ Fri, 01 Nov 2019 14:54:57: #2 finished! INFO @ Fri, 01 Nov 2019 14:54:57: #2 predicted fragment length is 118 bps INFO @ Fri, 01 Nov 2019 14:54:57: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 01 Nov 2019 14:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.05_model.r INFO @ Fri, 01 Nov 2019 14:54:57: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:54:58: 5000000 INFO @ Fri, 01 Nov 2019 14:55:02: 1000000 INFO @ Fri, 01 Nov 2019 14:55:05: 6000000 INFO @ Fri, 01 Nov 2019 14:55:09: 2000000 INFO @ Fri, 01 Nov 2019 14:55:11: 7000000 INFO @ Fri, 01 Nov 2019 14:55:16: 3000000 INFO @ Fri, 01 Nov 2019 14:55:19: 8000000 INFO @ Fri, 01 Nov 2019 14:55:23: 4000000 INFO @ Fri, 01 Nov 2019 14:55:25: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:55:25: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:55:25: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:55:25: #1 total tags in treatment: 8943008 INFO @ Fri, 01 Nov 2019 14:55:25: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:55:25: #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 14:55:25: #1 tags after filtering in treatment: 8943008 INFO @ Fri, 01 Nov 2019 14:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:55:25: #1 finished! INFO @ Fri, 01 Nov 2019 14:55:25: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:55:26: #2 number of paired peaks: 1095 INFO @ Fri, 01 Nov 2019 14:55:26: start model_add_line... INFO @ Fri, 01 Nov 2019 14:55:26: start X-correlation... INFO @ Fri, 01 Nov 2019 14:55:26: end of X-cor INFO @ Fri, 01 Nov 2019 14:55:26: #2 finished! INFO @ Fri, 01 Nov 2019 14:55:26: #2 predicted fragment length is 118 bps INFO @ Fri, 01 Nov 2019 14:55:26: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 01 Nov 2019 14:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.10_model.r INFO @ Fri, 01 Nov 2019 14:55:26: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:55:30: 5000000 INFO @ Fri, 01 Nov 2019 14:55:37: 6000000 INFO @ Fri, 01 Nov 2019 14:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.05_peaks.xls INFO @ Fri, 01 Nov 2019 14:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.05_summits.bed INFO @ Fri, 01 Nov 2019 14:55:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2734 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:55:44: 7000000 INFO @ Fri, 01 Nov 2019 14:55:51: 8000000 INFO @ Fri, 01 Nov 2019 14:55:53: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:55:58: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:55:58: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:55:58: #1 total tags in treatment: 8943008 INFO @ Fri, 01 Nov 2019 14:55:58: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:55:58: #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 14:55:58: #1 tags after filtering in treatment: 8943008 INFO @ Fri, 01 Nov 2019 14:55:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:55:58: #1 finished! INFO @ Fri, 01 Nov 2019 14:55:58: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:55:59: #2 number of paired peaks: 1095 INFO @ Fri, 01 Nov 2019 14:55:59: start model_add_line... INFO @ Fri, 01 Nov 2019 14:55:59: start X-correlation... INFO @ Fri, 01 Nov 2019 14:55:59: end of X-cor INFO @ Fri, 01 Nov 2019 14:55:59: #2 finished! INFO @ Fri, 01 Nov 2019 14:55:59: #2 predicted fragment length is 118 bps INFO @ Fri, 01 Nov 2019 14:55:59: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 01 Nov 2019 14:55:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.20_model.r INFO @ Fri, 01 Nov 2019 14:55:59: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:56:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.10_peaks.xls INFO @ Fri, 01 Nov 2019 14:56:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:56:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.10_summits.bed INFO @ Fri, 01 Nov 2019 14:56:06: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1220 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:56:26: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:56:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.20_peaks.xls INFO @ Fri, 01 Nov 2019 14:56:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:56:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247956/SRX5247956.20_summits.bed INFO @ Fri, 01 Nov 2019 14:56:39: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (501 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。