Job ID = 3785865 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:35:08 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 ) 2019-11-01T05:35:48 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 ) 2019-11-01T05:35:48 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 ) 2019-11-01T05:36:00 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 ) 2019-11-01T05:36:36 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 ) 2019-11-01T05:37:55 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 ) 2019-11-01T05:37:55 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 ) 2019-11-01T05:38:05 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 ) 2019-11-01T05:38:29 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 ) 2019-11-01T05:39:03 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 ) 2019-11-01T05:39:47 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 ) spots read : 9,024,515 reads read : 9,024,515 reads written : 9,024,515 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: 00:03:26 9024515 reads; of these: 9024515 (100.00%) were unpaired; of these: 613986 (6.80%) aligned 0 times 5532424 (61.30%) aligned exactly 1 time 2878105 (31.89%) aligned >1 times 93.20% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 385859 / 8410529 = 0.0459 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:47:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.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 14:47:48: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:47:48: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:47:56: 1000000 INFO @ Fri, 01 Nov 2019 14:48:03: 2000000 INFO @ Fri, 01 Nov 2019 14:48:11: 3000000 INFO @ Fri, 01 Nov 2019 14:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.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 14:48:17: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:48:17: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:48:19: 4000000 INFO @ Fri, 01 Nov 2019 14:48:25: 1000000 INFO @ Fri, 01 Nov 2019 14:48:27: 5000000 INFO @ Fri, 01 Nov 2019 14:48:33: 2000000 INFO @ Fri, 01 Nov 2019 14:48:35: 6000000 INFO @ Fri, 01 Nov 2019 14:48:42: 3000000 INFO @ Fri, 01 Nov 2019 14:48:43: 7000000 BedGraph に変換中... INFO @ Fri, 01 Nov 2019 14:48:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.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 14:48:47: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:48:47: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:48:50: 4000000 INFO @ Fri, 01 Nov 2019 14:48:51: 8000000 INFO @ Fri, 01 Nov 2019 14:48:51: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:48:51: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:48:51: #1 total tags in treatment: 8024670 INFO @ Fri, 01 Nov 2019 14:48:51: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:48:51: #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 14:48:51: #1 tags after filtering in treatment: 8024670 INFO @ Fri, 01 Nov 2019 14:48:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:48:51: #1 finished! INFO @ Fri, 01 Nov 2019 14:48:51: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:48:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:48:52: #2 number of paired peaks: 481 WARNING @ Fri, 01 Nov 2019 14:48:52: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Fri, 01 Nov 2019 14:48:52: start model_add_line... INFO @ Fri, 01 Nov 2019 14:48:52: start X-correlation... INFO @ Fri, 01 Nov 2019 14:48:52: end of X-cor INFO @ Fri, 01 Nov 2019 14:48:52: #2 finished! INFO @ Fri, 01 Nov 2019 14:48:52: #2 predicted fragment length is 134 bps INFO @ Fri, 01 Nov 2019 14:48:52: #2 alternative fragment length(s) may be 4,94,113,134 bps INFO @ Fri, 01 Nov 2019 14:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.05_model.r INFO @ Fri, 01 Nov 2019 14:48:52: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:48:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:48:57: 1000000 INFO @ Fri, 01 Nov 2019 14:48:58: 5000000 INFO @ Fri, 01 Nov 2019 14:49:06: 6000000 INFO @ Fri, 01 Nov 2019 14:49:06: 2000000 INFO @ Fri, 01 Nov 2019 14:49:14: 7000000 INFO @ Fri, 01 Nov 2019 14:49:16: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:49:16: 3000000 INFO @ Fri, 01 Nov 2019 14:49:22: 8000000 INFO @ Fri, 01 Nov 2019 14:49:22: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:49:22: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:49:22: #1 total tags in treatment: 8024670 INFO @ Fri, 01 Nov 2019 14:49:22: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:49:22: #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 14:49:22: #1 tags after filtering in treatment: 8024670 INFO @ Fri, 01 Nov 2019 14:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:49:22: #1 finished! INFO @ Fri, 01 Nov 2019 14:49:22: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:49:23: #2 number of paired peaks: 481 WARNING @ Fri, 01 Nov 2019 14:49:23: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Fri, 01 Nov 2019 14:49:23: start model_add_line... INFO @ Fri, 01 Nov 2019 14:49:23: start X-correlation... INFO @ Fri, 01 Nov 2019 14:49:23: end of X-cor INFO @ Fri, 01 Nov 2019 14:49:23: #2 finished! INFO @ Fri, 01 Nov 2019 14:49:23: #2 predicted fragment length is 134 bps INFO @ Fri, 01 Nov 2019 14:49:23: #2 alternative fragment length(s) may be 4,94,113,134 bps INFO @ Fri, 01 Nov 2019 14:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.10_model.r INFO @ Fri, 01 Nov 2019 14:49:23: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:49:26: 4000000 INFO @ Fri, 01 Nov 2019 14:49:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.05_peaks.xls INFO @ Fri, 01 Nov 2019 14:49:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:49:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.05_summits.bed INFO @ Fri, 01 Nov 2019 14:49:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2334 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:49:35: 5000000 INFO @ Fri, 01 Nov 2019 14:49:44: 6000000 INFO @ Fri, 01 Nov 2019 14:49:47: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:49:53: 7000000 INFO @ Fri, 01 Nov 2019 14:49:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.10_peaks.xls INFO @ Fri, 01 Nov 2019 14:49:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:49:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.10_summits.bed INFO @ Fri, 01 Nov 2019 14:49:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (823 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:50:02: 8000000 INFO @ Fri, 01 Nov 2019 14:50:02: #1 tag size is determined as 50 bps INFO @ Fri, 01 Nov 2019 14:50:02: #1 tag size = 50 INFO @ Fri, 01 Nov 2019 14:50:02: #1 total tags in treatment: 8024670 INFO @ Fri, 01 Nov 2019 14:50:02: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:50:02: #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 14:50:03: #1 tags after filtering in treatment: 8024670 INFO @ Fri, 01 Nov 2019 14:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:50:03: #1 finished! INFO @ Fri, 01 Nov 2019 14:50:03: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:50:03: #2 number of paired peaks: 481 WARNING @ Fri, 01 Nov 2019 14:50:03: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Fri, 01 Nov 2019 14:50:03: start model_add_line... INFO @ Fri, 01 Nov 2019 14:50:03: start X-correlation... INFO @ Fri, 01 Nov 2019 14:50:03: end of X-cor INFO @ Fri, 01 Nov 2019 14:50:03: #2 finished! INFO @ Fri, 01 Nov 2019 14:50:03: #2 predicted fragment length is 134 bps INFO @ Fri, 01 Nov 2019 14:50:03: #2 alternative fragment length(s) may be 4,94,113,134 bps INFO @ Fri, 01 Nov 2019 14:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.20_model.r INFO @ Fri, 01 Nov 2019 14:50:03: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:50:27: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.20_peaks.xls INFO @ Fri, 01 Nov 2019 14:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5247958/SRX5247958.20_summits.bed INFO @ Fri, 01 Nov 2019 14:50:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (219 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。