Job ID = 1293755 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:09:12 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 ) 2019-06-02T17:09:16 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 ) 2019-06-02T17:09:16 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 : 9,744,977 reads read : 9,744,977 reads written : 9,744,977 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: 00:06:12 9744977 reads; of these: 9744977 (100.00%) were unpaired; of these: 783572 (8.04%) aligned 0 times 3440033 (35.30%) aligned exactly 1 time 5521372 (56.66%) aligned >1 times 91.96% overall alignment rate Time searching: 00:06:12 Overall time: 00:06:12 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] 4848038 / 8961405 = 0.5410 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 02:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.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 02:19:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:19:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.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 02:19:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:19:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.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 02:19:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:19:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:19:18: 1000000 INFO @ Mon, 03 Jun 2019 02:19:20: 1000000 INFO @ Mon, 03 Jun 2019 02:19:23: 1000000 INFO @ Mon, 03 Jun 2019 02:19:27: 2000000 INFO @ Mon, 03 Jun 2019 02:19:32: 2000000 INFO @ Mon, 03 Jun 2019 02:19:35: 3000000 INFO @ Mon, 03 Jun 2019 02:19:36: 2000000 INFO @ Mon, 03 Jun 2019 02:19:45: 4000000 INFO @ Mon, 03 Jun 2019 02:19:46: 3000000 INFO @ Mon, 03 Jun 2019 02:19:46: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:19:46: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:19:46: #1 total tags in treatment: 4113367 INFO @ Mon, 03 Jun 2019 02:19:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:19:46: #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 02:19:46: #1 tags after filtering in treatment: 4113367 INFO @ Mon, 03 Jun 2019 02:19:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:19:46: #1 finished! INFO @ Mon, 03 Jun 2019 02:19:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:19:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:19:47: #2 number of paired peaks: 3403 INFO @ Mon, 03 Jun 2019 02:19:47: start model_add_line... INFO @ Mon, 03 Jun 2019 02:19:47: start X-correlation... INFO @ Mon, 03 Jun 2019 02:19:47: end of X-cor INFO @ Mon, 03 Jun 2019 02:19:47: #2 finished! INFO @ Mon, 03 Jun 2019 02:19:47: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 02:19:47: #2 alternative fragment length(s) may be 103,580 bps INFO @ Mon, 03 Jun 2019 02:19:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.10_model.r WARNING @ Mon, 03 Jun 2019 02:19:47: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:19:47: #2 You may need to consider one of the other alternative d(s): 103,580 WARNING @ Mon, 03 Jun 2019 02:19:47: #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 02:19:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:19:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:19:51: 3000000 INFO @ Mon, 03 Jun 2019 02:19:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:19:59: 4000000 INFO @ Mon, 03 Jun 2019 02:20:01: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:20:01: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:20:01: #1 total tags in treatment: 4113367 INFO @ Mon, 03 Jun 2019 02:20:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:20:01: #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 02:20:01: #1 tags after filtering in treatment: 4113367 INFO @ Mon, 03 Jun 2019 02:20:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:20:01: #1 finished! INFO @ Mon, 03 Jun 2019 02:20:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:20:02: #2 number of paired peaks: 3403 INFO @ Mon, 03 Jun 2019 02:20:02: start model_add_line... INFO @ Mon, 03 Jun 2019 02:20:02: start X-correlation... INFO @ Mon, 03 Jun 2019 02:20:02: end of X-cor INFO @ Mon, 03 Jun 2019 02:20:02: #2 finished! INFO @ Mon, 03 Jun 2019 02:20:02: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 02:20:02: #2 alternative fragment length(s) may be 103,580 bps INFO @ Mon, 03 Jun 2019 02:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.05_model.r WARNING @ Mon, 03 Jun 2019 02:20:02: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:20:02: #2 You may need to consider one of the other alternative d(s): 103,580 WARNING @ Mon, 03 Jun 2019 02:20:02: #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 02:20:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:20:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:20:04: 4000000 INFO @ Mon, 03 Jun 2019 02:20:05: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 02:20:05: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 02:20:05: #1 total tags in treatment: 4113367 INFO @ Mon, 03 Jun 2019 02:20:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:20:05: #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 02:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.10_summits.bed INFO @ Mon, 03 Jun 2019 02:20:05: Done! INFO @ Mon, 03 Jun 2019 02:20:05: #1 tags after filtering in treatment: 4113367 INFO @ Mon, 03 Jun 2019 02:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:20:05: #1 finished! INFO @ Mon, 03 Jun 2019 02:20:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:20:05: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:20:06: #2 number of paired peaks: 3403 INFO @ Mon, 03 Jun 2019 02:20:06: start model_add_line... INFO @ Mon, 03 Jun 2019 02:20:06: start X-correlation... INFO @ Mon, 03 Jun 2019 02:20:06: end of X-cor INFO @ Mon, 03 Jun 2019 02:20:06: #2 finished! INFO @ Mon, 03 Jun 2019 02:20:06: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 02:20:06: #2 alternative fragment length(s) may be 103,580 bps INFO @ Mon, 03 Jun 2019 02:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.20_model.r WARNING @ Mon, 03 Jun 2019 02:20:06: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:20:06: #2 You may need to consider one of the other alternative d(s): 103,580 WARNING @ Mon, 03 Jun 2019 02:20:06: #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 02:20:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:20:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:20:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:20:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:20:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:20:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.05_summits.bed INFO @ Mon, 03 Jun 2019 02:20:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3599 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:20:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:20:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:20:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1120699/SRX1120699.20_summits.bed INFO @ Mon, 03 Jun 2019 02:20:24: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (220 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。