Job ID = 1309268 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T14:16:12 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 : NET - Reading information from the socket failed ) 2019-06-03T14:16:12 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 : NET - Reading information from the socket failed ) 2019-06-03T14:16:12 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 ) 2019-06-03T14:16:12 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 ) 2019-06-03T14:16:12 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 : 5,884,662 reads read : 11,769,324 reads written : 5,884,662 reads 0-length : 5,884,662 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: 00:04:08 5884662 reads; of these: 5884662 (100.00%) were unpaired; of these: 181131 (3.08%) aligned 0 times 5123292 (87.06%) aligned exactly 1 time 580239 (9.86%) aligned >1 times 96.92% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 242573 / 5703531 = 0.0425 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 23:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.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 23:24:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:24:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.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 23:24:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:24:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.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 23:24:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:24:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:25:06: 1000000 INFO @ Mon, 03 Jun 2019 23:25:07: 1000000 INFO @ Mon, 03 Jun 2019 23:25:07: 1000000 INFO @ Mon, 03 Jun 2019 23:25:17: 2000000 INFO @ Mon, 03 Jun 2019 23:25:17: 2000000 INFO @ Mon, 03 Jun 2019 23:25:17: 2000000 INFO @ Mon, 03 Jun 2019 23:25:28: 3000000 INFO @ Mon, 03 Jun 2019 23:25:28: 3000000 INFO @ Mon, 03 Jun 2019 23:25:29: 3000000 INFO @ Mon, 03 Jun 2019 23:25:39: 4000000 INFO @ Mon, 03 Jun 2019 23:25:39: 4000000 INFO @ Mon, 03 Jun 2019 23:25:39: 4000000 INFO @ Mon, 03 Jun 2019 23:25:50: 5000000 INFO @ Mon, 03 Jun 2019 23:25:50: 5000000 INFO @ Mon, 03 Jun 2019 23:25:50: 5000000 INFO @ Mon, 03 Jun 2019 23:25:55: #1 tag size is determined as 145 bps INFO @ Mon, 03 Jun 2019 23:25:55: #1 tag size = 145 INFO @ Mon, 03 Jun 2019 23:25:55: #1 total tags in treatment: 5460958 INFO @ Mon, 03 Jun 2019 23:25:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:25:55: #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 23:25:55: #1 tags after filtering in treatment: 5460958 INFO @ Mon, 03 Jun 2019 23:25:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:25:55: #1 finished! INFO @ Mon, 03 Jun 2019 23:25:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:25:55: #1 tag size is determined as 145 bps INFO @ Mon, 03 Jun 2019 23:25:55: #1 tag size = 145 INFO @ Mon, 03 Jun 2019 23:25:55: #1 total tags in treatment: 5460958 INFO @ Mon, 03 Jun 2019 23:25:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:25:55: #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 23:25:55: #1 tags after filtering in treatment: 5460958 INFO @ Mon, 03 Jun 2019 23:25:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:25:55: #1 finished! INFO @ Mon, 03 Jun 2019 23:25:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:25:55: #1 tag size is determined as 145 bps INFO @ Mon, 03 Jun 2019 23:25:55: #1 tag size = 145 INFO @ Mon, 03 Jun 2019 23:25:55: #1 total tags in treatment: 5460958 INFO @ Mon, 03 Jun 2019 23:25:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:25:55: #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 23:25:55: #1 tags after filtering in treatment: 5460958 INFO @ Mon, 03 Jun 2019 23:25:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:25:55: #1 finished! INFO @ Mon, 03 Jun 2019 23:25:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:25:56: #2 number of paired peaks: 1435 INFO @ Mon, 03 Jun 2019 23:25:56: start model_add_line... INFO @ Mon, 03 Jun 2019 23:25:56: start X-correlation... INFO @ Mon, 03 Jun 2019 23:25:56: end of X-cor INFO @ Mon, 03 Jun 2019 23:25:56: #2 finished! INFO @ Mon, 03 Jun 2019 23:25:56: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 23:25:56: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 23:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.10_model.r WARNING @ Mon, 03 Jun 2019 23:25:56: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:25:56: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Mon, 03 Jun 2019 23:25:56: #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 23:25:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:25:56: #2 number of paired peaks: 1435 INFO @ Mon, 03 Jun 2019 23:25:56: start model_add_line... INFO @ Mon, 03 Jun 2019 23:25:56: start X-correlation... INFO @ Mon, 03 Jun 2019 23:25:56: end of X-cor INFO @ Mon, 03 Jun 2019 23:25:56: #2 finished! INFO @ Mon, 03 Jun 2019 23:25:56: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 23:25:56: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 23:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.05_model.r WARNING @ Mon, 03 Jun 2019 23:25:56: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:25:56: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Mon, 03 Jun 2019 23:25:56: #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 23:25:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:25:56: #2 number of paired peaks: 1435 INFO @ Mon, 03 Jun 2019 23:25:56: start model_add_line... INFO @ Mon, 03 Jun 2019 23:25:56: start X-correlation... INFO @ Mon, 03 Jun 2019 23:25:56: end of X-cor INFO @ Mon, 03 Jun 2019 23:25:56: #2 finished! INFO @ Mon, 03 Jun 2019 23:25:56: #2 predicted fragment length is 167 bps INFO @ Mon, 03 Jun 2019 23:25:56: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 03 Jun 2019 23:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.20_model.r WARNING @ Mon, 03 Jun 2019 23:25:56: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:25:56: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Mon, 03 Jun 2019 23:25:56: #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 23:25:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:26:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:26:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:26:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.10_summits.bed INFO @ Mon, 03 Jun 2019 23:26:22: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (3059 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:26:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:26:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.20_summits.bed INFO @ Mon, 03 Jun 2019 23:26:23: Done! INFO @ Mon, 03 Jun 2019 23:26:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.05_peaks.xls pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (936 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:26:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:26:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX864529/SRX864529.05_summits.bed INFO @ Mon, 03 Jun 2019 23:26:23: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (6991 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。