Job ID = 1293680 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:32:30 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 ) 2019-06-02T16:32:30 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 ) 2019-06-02T16:32:30 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 ) 2019-06-02T16:32:30 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 ) 2019-06-02T16:35:30 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 ) 2019-06-02T16:35:30 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 ) 2019-06-02T16:38:47 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 : 4,660,093 reads read : 9,320,186 reads written : 4,660,093 reads 0-length : 4,660,093 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: 00:05:13 4660093 reads; of these: 4660093 (100.00%) were unpaired; of these: 277863 (5.96%) aligned 0 times 3715907 (79.74%) aligned exactly 1 time 666323 (14.30%) aligned >1 times 94.04% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 214738 / 4382230 = 0.0490 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 01:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.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 01:48:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:48:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.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 01:48:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:48:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.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 01:48:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:48:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:48:32: 1000000 INFO @ Mon, 03 Jun 2019 01:48:34: 1000000 INFO @ Mon, 03 Jun 2019 01:48:34: 1000000 INFO @ Mon, 03 Jun 2019 01:48:47: 2000000 INFO @ Mon, 03 Jun 2019 01:48:49: 2000000 INFO @ Mon, 03 Jun 2019 01:48:51: 2000000 INFO @ Mon, 03 Jun 2019 01:49:01: 3000000 INFO @ Mon, 03 Jun 2019 01:49:04: 3000000 INFO @ Mon, 03 Jun 2019 01:49:06: 3000000 INFO @ Mon, 03 Jun 2019 01:49:15: 4000000 INFO @ Mon, 03 Jun 2019 01:49:18: #1 tag size is determined as 149 bps INFO @ Mon, 03 Jun 2019 01:49:18: #1 tag size = 149 INFO @ Mon, 03 Jun 2019 01:49:18: #1 total tags in treatment: 4167492 INFO @ Mon, 03 Jun 2019 01:49:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:49:18: #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 01:49:18: #1 tags after filtering in treatment: 4167492 INFO @ Mon, 03 Jun 2019 01:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:49:18: #1 finished! INFO @ Mon, 03 Jun 2019 01:49:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:49:18: #2 number of paired peaks: 617 WARNING @ Mon, 03 Jun 2019 01:49:18: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Mon, 03 Jun 2019 01:49:18: start model_add_line... INFO @ Mon, 03 Jun 2019 01:49:18: start X-correlation... INFO @ Mon, 03 Jun 2019 01:49:18: end of X-cor INFO @ Mon, 03 Jun 2019 01:49:18: #2 finished! INFO @ Mon, 03 Jun 2019 01:49:18: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 01:49:18: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 03 Jun 2019 01:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.10_model.r WARNING @ Mon, 03 Jun 2019 01:49:18: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:49:18: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Mon, 03 Jun 2019 01:49:18: #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 01:49:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:49:19: 4000000 INFO @ Mon, 03 Jun 2019 01:49:22: #1 tag size is determined as 149 bps INFO @ Mon, 03 Jun 2019 01:49:22: #1 tag size = 149 INFO @ Mon, 03 Jun 2019 01:49:22: #1 total tags in treatment: 4167492 INFO @ Mon, 03 Jun 2019 01:49:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:49:22: #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 01:49:22: #1 tags after filtering in treatment: 4167492 INFO @ Mon, 03 Jun 2019 01:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:49:22: #1 finished! INFO @ Mon, 03 Jun 2019 01:49:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:49:22: 4000000 INFO @ Mon, 03 Jun 2019 01:49:22: #2 number of paired peaks: 617 WARNING @ Mon, 03 Jun 2019 01:49:22: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Mon, 03 Jun 2019 01:49:22: start model_add_line... INFO @ Mon, 03 Jun 2019 01:49:22: start X-correlation... INFO @ Mon, 03 Jun 2019 01:49:22: end of X-cor INFO @ Mon, 03 Jun 2019 01:49:22: #2 finished! INFO @ Mon, 03 Jun 2019 01:49:22: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 01:49:22: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 03 Jun 2019 01:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.05_model.r WARNING @ Mon, 03 Jun 2019 01:49:22: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:49:22: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Mon, 03 Jun 2019 01:49:22: #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 01:49:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:49:24: #1 tag size is determined as 149 bps INFO @ Mon, 03 Jun 2019 01:49:24: #1 tag size = 149 INFO @ Mon, 03 Jun 2019 01:49:24: #1 total tags in treatment: 4167492 INFO @ Mon, 03 Jun 2019 01:49:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:49:24: #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 01:49:24: #1 tags after filtering in treatment: 4167492 INFO @ Mon, 03 Jun 2019 01:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:49:24: #1 finished! INFO @ Mon, 03 Jun 2019 01:49:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:49:25: #2 number of paired peaks: 617 WARNING @ Mon, 03 Jun 2019 01:49:25: Fewer paired peaks (617) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 617 pairs to build model! INFO @ Mon, 03 Jun 2019 01:49:25: start model_add_line... INFO @ Mon, 03 Jun 2019 01:49:25: start X-correlation... INFO @ Mon, 03 Jun 2019 01:49:25: end of X-cor INFO @ Mon, 03 Jun 2019 01:49:25: #2 finished! INFO @ Mon, 03 Jun 2019 01:49:25: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 01:49:25: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 03 Jun 2019 01:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.20_model.r WARNING @ Mon, 03 Jun 2019 01:49:25: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:49:25: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Mon, 03 Jun 2019 01:49:25: #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 01:49:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:49:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:49:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:49:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.10_summits.bed INFO @ Mon, 03 Jun 2019 01:49:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:49:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:49:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:49:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.05_summits.bed INFO @ Mon, 03 Jun 2019 01:49:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2973 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:49:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:49:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:49:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091591/SRX1091591.20_summits.bed INFO @ Mon, 03 Jun 2019 01:49:45: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (234 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。