Job ID = 1294510 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:31:56 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 ) 2019-06-02T23:33:25 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 ) 2019-06-02T23:33:25 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 ) 2019-06-02T23:34:09 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 ) 2019-06-02T23:35:23 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 ) 2019-06-02T23:35:40 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 ) 2019-06-02T23:36:01 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 ) 2019-06-02T23:36:01 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 ) 2019-06-02T23:36:05 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 ) 2019-06-02T23:37:10 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 ) 2019-06-02T23:41:18 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 ) spots read : 19,977,921 reads read : 19,977,921 reads written : 19,977,921 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: 00:05:24 19977921 reads; of these: 19977921 (100.00%) were unpaired; of these: 1742583 (8.72%) aligned 0 times 16727695 (83.73%) aligned exactly 1 time 1507643 (7.55%) aligned >1 times 91.28% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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 8 files... [bam_rmdupse_core] 2226796 / 18235338 = 0.1221 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 08:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.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 08:55:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.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 08:55:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:55:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.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 08:55:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:55:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:55:45: 1000000 INFO @ Mon, 03 Jun 2019 08:55:45: 1000000 INFO @ Mon, 03 Jun 2019 08:55:46: 1000000 INFO @ Mon, 03 Jun 2019 08:55:56: 2000000 INFO @ Mon, 03 Jun 2019 08:55:57: 2000000 INFO @ Mon, 03 Jun 2019 08:55:58: 2000000 INFO @ Mon, 03 Jun 2019 08:56:06: 3000000 INFO @ Mon, 03 Jun 2019 08:56:08: 3000000 INFO @ Mon, 03 Jun 2019 08:56:09: 3000000 INFO @ Mon, 03 Jun 2019 08:56:16: 4000000 INFO @ Mon, 03 Jun 2019 08:56:18: 4000000 INFO @ Mon, 03 Jun 2019 08:56:20: 4000000 INFO @ Mon, 03 Jun 2019 08:56:25: 5000000 INFO @ Mon, 03 Jun 2019 08:56:28: 5000000 INFO @ Mon, 03 Jun 2019 08:56:31: 5000000 INFO @ Mon, 03 Jun 2019 08:56:34: 6000000 INFO @ Mon, 03 Jun 2019 08:56:38: 6000000 INFO @ Mon, 03 Jun 2019 08:56:41: 6000000 INFO @ Mon, 03 Jun 2019 08:56:44: 7000000 INFO @ Mon, 03 Jun 2019 08:56:48: 7000000 INFO @ Mon, 03 Jun 2019 08:56:52: 7000000 INFO @ Mon, 03 Jun 2019 08:56:53: 8000000 INFO @ Mon, 03 Jun 2019 08:56:59: 8000000 INFO @ Mon, 03 Jun 2019 08:57:02: 8000000 INFO @ Mon, 03 Jun 2019 08:57:02: 9000000 INFO @ Mon, 03 Jun 2019 08:57:09: 9000000 INFO @ Mon, 03 Jun 2019 08:57:13: 10000000 INFO @ Mon, 03 Jun 2019 08:57:13: 9000000 INFO @ Mon, 03 Jun 2019 08:57:20: 10000000 INFO @ Mon, 03 Jun 2019 08:57:22: 11000000 INFO @ Mon, 03 Jun 2019 08:57:25: 10000000 INFO @ Mon, 03 Jun 2019 08:57:30: 11000000 INFO @ Mon, 03 Jun 2019 08:57:31: 12000000 INFO @ Mon, 03 Jun 2019 08:57:35: 11000000 INFO @ Mon, 03 Jun 2019 08:57:40: 12000000 INFO @ Mon, 03 Jun 2019 08:57:40: 13000000 INFO @ Mon, 03 Jun 2019 08:57:45: 12000000 INFO @ Mon, 03 Jun 2019 08:57:50: 13000000 INFO @ Mon, 03 Jun 2019 08:57:50: 14000000 INFO @ Mon, 03 Jun 2019 08:57:56: 13000000 INFO @ Mon, 03 Jun 2019 08:57:59: 14000000 INFO @ Mon, 03 Jun 2019 08:58:00: 15000000 INFO @ Mon, 03 Jun 2019 08:58:06: 14000000 INFO @ Mon, 03 Jun 2019 08:58:08: 16000000 INFO @ Mon, 03 Jun 2019 08:58:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:58:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:58:09: #1 total tags in treatment: 16008542 INFO @ Mon, 03 Jun 2019 08:58:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:58:09: #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 08:58:09: #1 tags after filtering in treatment: 16008542 INFO @ Mon, 03 Jun 2019 08:58:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:58:09: #1 finished! INFO @ Mon, 03 Jun 2019 08:58:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:58:09: 15000000 INFO @ Mon, 03 Jun 2019 08:58:11: #2 number of paired peaks: 502 WARNING @ Mon, 03 Jun 2019 08:58:11: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 03 Jun 2019 08:58:11: start model_add_line... INFO @ Mon, 03 Jun 2019 08:58:11: start X-correlation... INFO @ Mon, 03 Jun 2019 08:58:11: end of X-cor INFO @ Mon, 03 Jun 2019 08:58:11: #2 finished! INFO @ Mon, 03 Jun 2019 08:58:11: #2 predicted fragment length is 184 bps INFO @ Mon, 03 Jun 2019 08:58:11: #2 alternative fragment length(s) may be 184 bps INFO @ Mon, 03 Jun 2019 08:58:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.20_model.r INFO @ Mon, 03 Jun 2019 08:58:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:58:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:58:16: 15000000 INFO @ Mon, 03 Jun 2019 08:58:19: 16000000 INFO @ Mon, 03 Jun 2019 08:58:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:58:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:58:19: #1 total tags in treatment: 16008542 INFO @ Mon, 03 Jun 2019 08:58:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:58:19: #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 08:58:19: #1 tags after filtering in treatment: 16008542 INFO @ Mon, 03 Jun 2019 08:58:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:58:19: #1 finished! INFO @ Mon, 03 Jun 2019 08:58:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:58:21: #2 number of paired peaks: 502 WARNING @ Mon, 03 Jun 2019 08:58:21: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 03 Jun 2019 08:58:21: start model_add_line... INFO @ Mon, 03 Jun 2019 08:58:21: start X-correlation... INFO @ Mon, 03 Jun 2019 08:58:21: end of X-cor INFO @ Mon, 03 Jun 2019 08:58:21: #2 finished! INFO @ Mon, 03 Jun 2019 08:58:21: #2 predicted fragment length is 184 bps INFO @ Mon, 03 Jun 2019 08:58:21: #2 alternative fragment length(s) may be 184 bps INFO @ Mon, 03 Jun 2019 08:58:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.05_model.r INFO @ Mon, 03 Jun 2019 08:58:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:58:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:58:26: 16000000 INFO @ Mon, 03 Jun 2019 08:58:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:58:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:58:26: #1 total tags in treatment: 16008542 INFO @ Mon, 03 Jun 2019 08:58:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:58:26: #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 08:58:26: #1 tags after filtering in treatment: 16008542 INFO @ Mon, 03 Jun 2019 08:58:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:58:26: #1 finished! INFO @ Mon, 03 Jun 2019 08:58:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:58:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:58:28: #2 number of paired peaks: 502 WARNING @ Mon, 03 Jun 2019 08:58:28: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 03 Jun 2019 08:58:28: start model_add_line... INFO @ Mon, 03 Jun 2019 08:58:28: start X-correlation... INFO @ Mon, 03 Jun 2019 08:58:28: end of X-cor INFO @ Mon, 03 Jun 2019 08:58:28: #2 finished! INFO @ Mon, 03 Jun 2019 08:58:28: #2 predicted fragment length is 184 bps INFO @ Mon, 03 Jun 2019 08:58:28: #2 alternative fragment length(s) may be 184 bps INFO @ Mon, 03 Jun 2019 08:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.10_model.r INFO @ Mon, 03 Jun 2019 08:58:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:58:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:59:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:59:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.20_summits.bed INFO @ Mon, 03 Jun 2019 08:59:21: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3383 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:59:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:59:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:59:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.05_summits.bed INFO @ Mon, 03 Jun 2019 08:59:33: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8215 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:59:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:59:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:59:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287708/SRX287708.10_summits.bed INFO @ Mon, 03 Jun 2019 08:59:41: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5722 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。