Job ID = 1293375 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T15:10:15 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 : 69,954,080 reads read : 69,954,080 reads written : 69,954,080 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: 00:18:40 69954080 reads; of these: 69954080 (100.00%) were unpaired; of these: 57442610 (82.11%) aligned 0 times 11018248 (15.75%) aligned exactly 1 time 1493222 (2.13%) aligned >1 times 17.89% overall alignment rate Time searching: 00:18:40 Overall time: 00:18:40 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] 11797856 / 12511470 = 0.9430 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 00:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.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 00:44:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:44:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.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 00:44:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:44:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.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 00:44:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:44:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:44:33: #1 tag size is determined as 99 bps INFO @ Mon, 03 Jun 2019 00:44:33: #1 tag size = 99 INFO @ Mon, 03 Jun 2019 00:44:33: #1 total tags in treatment: 713614 INFO @ Mon, 03 Jun 2019 00:44:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:44:33: #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 00:44:33: #1 tags after filtering in treatment: 713614 INFO @ Mon, 03 Jun 2019 00:44:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:44:33: #1 finished! INFO @ Mon, 03 Jun 2019 00:44:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:44:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:44:33: #2 number of paired peaks: 3478 INFO @ Mon, 03 Jun 2019 00:44:33: start model_add_line... INFO @ Mon, 03 Jun 2019 00:44:33: #1 tag size is determined as 99 bps INFO @ Mon, 03 Jun 2019 00:44:33: #1 tag size = 99 INFO @ Mon, 03 Jun 2019 00:44:33: #1 total tags in treatment: 713614 INFO @ Mon, 03 Jun 2019 00:44:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:44:33: #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 00:44:33: start X-correlation... INFO @ Mon, 03 Jun 2019 00:44:33: #1 tags after filtering in treatment: 713614 INFO @ Mon, 03 Jun 2019 00:44:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:44:33: #1 finished! INFO @ Mon, 03 Jun 2019 00:44:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:44:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:44:33: end of X-cor INFO @ Mon, 03 Jun 2019 00:44:33: #2 finished! INFO @ Mon, 03 Jun 2019 00:44:33: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 00:44:33: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 00:44:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.05_model.r WARNING @ Mon, 03 Jun 2019 00:44:33: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 00:44:33: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Mon, 03 Jun 2019 00:44:33: #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 00:44:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:44:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:44:33: #2 number of paired peaks: 3478 INFO @ Mon, 03 Jun 2019 00:44:33: start model_add_line... INFO @ Mon, 03 Jun 2019 00:44:33: start X-correlation... INFO @ Mon, 03 Jun 2019 00:44:33: end of X-cor INFO @ Mon, 03 Jun 2019 00:44:33: #2 finished! INFO @ Mon, 03 Jun 2019 00:44:33: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 00:44:33: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 00:44:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.20_model.r WARNING @ Mon, 03 Jun 2019 00:44:33: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 00:44:33: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Mon, 03 Jun 2019 00:44:33: #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 00:44:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:44:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:44:35: #1 tag size is determined as 99 bps INFO @ Mon, 03 Jun 2019 00:44:35: #1 tag size = 99 INFO @ Mon, 03 Jun 2019 00:44:35: #1 total tags in treatment: 713614 INFO @ Mon, 03 Jun 2019 00:44:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:44:35: #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 00:44:35: #1 tags after filtering in treatment: 713614 INFO @ Mon, 03 Jun 2019 00:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 00:44:35: #1 finished! INFO @ Mon, 03 Jun 2019 00:44:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:44:35: #2 number of paired peaks: 3478 INFO @ Mon, 03 Jun 2019 00:44:35: start model_add_line... INFO @ Mon, 03 Jun 2019 00:44:35: start X-correlation... INFO @ Mon, 03 Jun 2019 00:44:36: end of X-cor INFO @ Mon, 03 Jun 2019 00:44:36: #2 finished! INFO @ Mon, 03 Jun 2019 00:44:36: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 00:44:36: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 00:44:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.10_model.r WARNING @ Mon, 03 Jun 2019 00:44:36: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 00:44:36: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Mon, 03 Jun 2019 00:44:36: #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 00:44:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:44:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:44:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.05_summits.bed INFO @ Mon, 03 Jun 2019 00:44:37: Done! INFO @ Mon, 03 Jun 2019 00:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.20_summits.bed INFO @ Mon, 03 Jun 2019 00:44:37: Done! pass1 - making usageList (11 chroms): 2 millis pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (135 records, 4 fields): 2 millis pass2 - checking and writing primary data (1256 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 00:44:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1918289/ERX1918289.10_summits.bed INFO @ Mon, 03 Jun 2019 00:44:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (385 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。