Job ID = 1294477 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:14:30 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 ) 2019-06-02T23:14:30 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 ) 2019-06-02T23:14:30 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 ) 2019-06-02T23:15:34 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 ) 2019-06-02T23:15:34 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 ) 2019-06-02T23:15:35 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 ) 2019-06-02T23:17:08 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 ) 2019-06-02T23:17:08 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 ) 2019-06-02T23:17:40 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 ) 2019-06-02T23:17:40 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 ) 2019-06-02T23:19:11 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 ) 2019-06-02T23:20:00 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 ) spots read : 14,983,362 reads read : 14,983,362 reads written : 14,983,362 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: 00:12:03 14983362 reads; of these: 14983362 (100.00%) were unpaired; of these: 671073 (4.48%) aligned 0 times 2837702 (18.94%) aligned exactly 1 time 11474587 (76.58%) aligned >1 times 95.52% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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] 3909416 / 14312289 = 0.2732 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 08:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.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 08:39:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:39:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.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 08:39:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:39:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.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 08:39:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:39:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:39:46: 1000000 INFO @ Mon, 03 Jun 2019 08:39:46: 1000000 INFO @ Mon, 03 Jun 2019 08:39:47: 1000000 INFO @ Mon, 03 Jun 2019 08:39:54: 2000000 INFO @ Mon, 03 Jun 2019 08:39:54: 2000000 INFO @ Mon, 03 Jun 2019 08:39:55: 2000000 INFO @ Mon, 03 Jun 2019 08:40:01: 3000000 INFO @ Mon, 03 Jun 2019 08:40:01: 3000000 INFO @ Mon, 03 Jun 2019 08:40:03: 3000000 INFO @ Mon, 03 Jun 2019 08:40:08: 4000000 INFO @ Mon, 03 Jun 2019 08:40:08: 4000000 INFO @ Mon, 03 Jun 2019 08:40:10: 4000000 INFO @ Mon, 03 Jun 2019 08:40:15: 5000000 INFO @ Mon, 03 Jun 2019 08:40:15: 5000000 INFO @ Mon, 03 Jun 2019 08:40:17: 5000000 INFO @ Mon, 03 Jun 2019 08:40:22: 6000000 INFO @ Mon, 03 Jun 2019 08:40:22: 6000000 INFO @ Mon, 03 Jun 2019 08:40:24: 6000000 INFO @ Mon, 03 Jun 2019 08:40:29: 7000000 INFO @ Mon, 03 Jun 2019 08:40:30: 7000000 INFO @ Mon, 03 Jun 2019 08:40:31: 7000000 INFO @ Mon, 03 Jun 2019 08:40:36: 8000000 INFO @ Mon, 03 Jun 2019 08:40:37: 8000000 INFO @ Mon, 03 Jun 2019 08:40:38: 8000000 INFO @ Mon, 03 Jun 2019 08:40:44: 9000000 INFO @ Mon, 03 Jun 2019 08:40:44: 9000000 INFO @ Mon, 03 Jun 2019 08:40:45: 9000000 INFO @ Mon, 03 Jun 2019 08:40:51: 10000000 INFO @ Mon, 03 Jun 2019 08:40:51: 10000000 INFO @ Mon, 03 Jun 2019 08:40:52: 10000000 INFO @ Mon, 03 Jun 2019 08:40:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:40:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:40:54: #1 total tags in treatment: 10402873 INFO @ Mon, 03 Jun 2019 08:40:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:40:54: #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 08:40:54: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:40:54: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:40:54: #1 total tags in treatment: 10402873 INFO @ Mon, 03 Jun 2019 08:40:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:40:54: #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 08:40:54: #1 tags after filtering in treatment: 10402873 INFO @ Mon, 03 Jun 2019 08:40:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:40:54: #1 finished! INFO @ Mon, 03 Jun 2019 08:40:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:40:54: #1 tags after filtering in treatment: 10402873 INFO @ Mon, 03 Jun 2019 08:40:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:40:54: #1 finished! INFO @ Mon, 03 Jun 2019 08:40:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:40:55: #2 number of paired peaks: 1366 INFO @ Mon, 03 Jun 2019 08:40:55: start model_add_line... INFO @ Mon, 03 Jun 2019 08:40:55: #2 number of paired peaks: 1366 INFO @ Mon, 03 Jun 2019 08:40:55: start model_add_line... INFO @ Mon, 03 Jun 2019 08:40:55: start X-correlation... INFO @ Mon, 03 Jun 2019 08:40:55: end of X-cor INFO @ Mon, 03 Jun 2019 08:40:55: #2 finished! INFO @ Mon, 03 Jun 2019 08:40:55: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:40:55: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:40:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.05_model.r WARNING @ Mon, 03 Jun 2019 08:40:55: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:40:55: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:40:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:40:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:40:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:40:55: start X-correlation... INFO @ Mon, 03 Jun 2019 08:40:55: end of X-cor INFO @ Mon, 03 Jun 2019 08:40:55: #2 finished! INFO @ Mon, 03 Jun 2019 08:40:55: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:40:55: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:40:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.10_model.r WARNING @ Mon, 03 Jun 2019 08:40:55: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:40:55: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:40:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:40:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:40:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:40:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:40:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:40:55: #1 total tags in treatment: 10402873 INFO @ Mon, 03 Jun 2019 08:40:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:40:55: #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 08:40:55: #1 tags after filtering in treatment: 10402873 INFO @ Mon, 03 Jun 2019 08:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:40:55: #1 finished! INFO @ Mon, 03 Jun 2019 08:40:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:40:56: #2 number of paired peaks: 1366 INFO @ Mon, 03 Jun 2019 08:40:56: start model_add_line... INFO @ Mon, 03 Jun 2019 08:40:56: start X-correlation... INFO @ Mon, 03 Jun 2019 08:40:56: end of X-cor INFO @ Mon, 03 Jun 2019 08:40:56: #2 finished! INFO @ Mon, 03 Jun 2019 08:40:56: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:40:56: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:40:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.20_model.r WARNING @ Mon, 03 Jun 2019 08:40:56: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:40:56: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:40:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:40:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:41:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:41:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:41:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.10_summits.bed INFO @ Mon, 03 Jun 2019 08:41:37: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1881 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.05_summits.bed INFO @ Mon, 03 Jun 2019 08:41:37: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4649 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:41:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:41:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:41:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287676/SRX287676.20_summits.bed INFO @ Mon, 03 Jun 2019 08:41:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1229 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。