Job ID = 1295339 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T04:16:52 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 ) 2019-06-03T04:16:52 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 : 25,341,638 reads read : 25,341,638 reads written : 25,341,638 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: 00:11:59 25341638 reads; of these: 25341638 (100.00%) were unpaired; of these: 8856166 (34.95%) aligned 0 times 6206683 (24.49%) aligned exactly 1 time 10278789 (40.56%) aligned >1 times 65.05% overall alignment rate Time searching: 00:11:59 Overall time: 00:11:59 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] 7094448 / 16485472 = 0.4303 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 13:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.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 13:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.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 13:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.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 13:38:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:38:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:38:57: 1000000 INFO @ Mon, 03 Jun 2019 13:38:58: 1000000 INFO @ Mon, 03 Jun 2019 13:38:58: 1000000 INFO @ Mon, 03 Jun 2019 13:39:07: 2000000 INFO @ Mon, 03 Jun 2019 13:39:09: 2000000 INFO @ Mon, 03 Jun 2019 13:39:10: 2000000 INFO @ Mon, 03 Jun 2019 13:39:17: 3000000 INFO @ Mon, 03 Jun 2019 13:39:20: 3000000 INFO @ Mon, 03 Jun 2019 13:39:22: 3000000 INFO @ Mon, 03 Jun 2019 13:39:28: 4000000 INFO @ Mon, 03 Jun 2019 13:39:30: 4000000 INFO @ Mon, 03 Jun 2019 13:39:34: 4000000 INFO @ Mon, 03 Jun 2019 13:39:37: 5000000 INFO @ Mon, 03 Jun 2019 13:39:41: 5000000 INFO @ Mon, 03 Jun 2019 13:39:45: 5000000 INFO @ Mon, 03 Jun 2019 13:39:47: 6000000 INFO @ Mon, 03 Jun 2019 13:39:51: 6000000 INFO @ Mon, 03 Jun 2019 13:39:56: 6000000 INFO @ Mon, 03 Jun 2019 13:39:57: 7000000 INFO @ Mon, 03 Jun 2019 13:40:01: 7000000 INFO @ Mon, 03 Jun 2019 13:40:07: 7000000 INFO @ Mon, 03 Jun 2019 13:40:07: 8000000 INFO @ Mon, 03 Jun 2019 13:40:11: 8000000 INFO @ Mon, 03 Jun 2019 13:40:17: 9000000 INFO @ Mon, 03 Jun 2019 13:40:18: 8000000 INFO @ Mon, 03 Jun 2019 13:40:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:40:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:40:21: #1 total tags in treatment: 9391024 INFO @ Mon, 03 Jun 2019 13:40:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:40:21: #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 13:40:21: #1 tags after filtering in treatment: 9391024 INFO @ Mon, 03 Jun 2019 13:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:40:21: #1 finished! INFO @ Mon, 03 Jun 2019 13:40:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:40:22: 9000000 INFO @ Mon, 03 Jun 2019 13:40:22: #2 number of paired peaks: 1110 INFO @ Mon, 03 Jun 2019 13:40:22: start model_add_line... INFO @ Mon, 03 Jun 2019 13:40:22: start X-correlation... INFO @ Mon, 03 Jun 2019 13:40:22: end of X-cor INFO @ Mon, 03 Jun 2019 13:40:22: #2 finished! INFO @ Mon, 03 Jun 2019 13:40:22: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:40:22: #2 alternative fragment length(s) may be 3,52,516 bps INFO @ Mon, 03 Jun 2019 13:40:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.05_model.r WARNING @ Mon, 03 Jun 2019 13:40:22: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:40:22: #2 You may need to consider one of the other alternative d(s): 3,52,516 WARNING @ Mon, 03 Jun 2019 13:40:22: #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 13:40:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:40:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:40:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:40:26: #1 total tags in treatment: 9391024 INFO @ Mon, 03 Jun 2019 13:40:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:40:26: #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 13:40:26: #1 tags after filtering in treatment: 9391024 INFO @ Mon, 03 Jun 2019 13:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:40:26: #1 finished! INFO @ Mon, 03 Jun 2019 13:40:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:40:27: #2 number of paired peaks: 1110 INFO @ Mon, 03 Jun 2019 13:40:27: start model_add_line... INFO @ Mon, 03 Jun 2019 13:40:27: start X-correlation... INFO @ Mon, 03 Jun 2019 13:40:27: end of X-cor INFO @ Mon, 03 Jun 2019 13:40:27: #2 finished! INFO @ Mon, 03 Jun 2019 13:40:27: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:40:27: #2 alternative fragment length(s) may be 3,52,516 bps INFO @ Mon, 03 Jun 2019 13:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.10_model.r WARNING @ Mon, 03 Jun 2019 13:40:27: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:40:27: #2 You may need to consider one of the other alternative d(s): 3,52,516 WARNING @ Mon, 03 Jun 2019 13:40:27: #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 13:40:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:40:29: 9000000 INFO @ Mon, 03 Jun 2019 13:40:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:40:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:40:33: #1 total tags in treatment: 9391024 INFO @ Mon, 03 Jun 2019 13:40:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:40:33: #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 13:40:33: #1 tags after filtering in treatment: 9391024 INFO @ Mon, 03 Jun 2019 13:40:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:40:33: #1 finished! INFO @ Mon, 03 Jun 2019 13:40:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:40:34: #2 number of paired peaks: 1110 INFO @ Mon, 03 Jun 2019 13:40:34: start model_add_line... INFO @ Mon, 03 Jun 2019 13:40:34: start X-correlation... INFO @ Mon, 03 Jun 2019 13:40:34: end of X-cor INFO @ Mon, 03 Jun 2019 13:40:34: #2 finished! INFO @ Mon, 03 Jun 2019 13:40:34: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:40:34: #2 alternative fragment length(s) may be 3,52,516 bps INFO @ Mon, 03 Jun 2019 13:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.20_model.r WARNING @ Mon, 03 Jun 2019 13:40:34: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:40:34: #2 You may need to consider one of the other alternative d(s): 3,52,516 WARNING @ Mon, 03 Jun 2019 13:40:34: #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 13:40:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:40:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:40:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:40:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:41:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:41:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:41:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:41:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.05_summits.bed INFO @ Mon, 03 Jun 2019 13:41:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2819 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:41:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:41:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:41:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.10_summits.bed INFO @ Mon, 03 Jun 2019 13:41:08: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1399 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335495/SRX335495.20_summits.bed INFO @ Mon, 03 Jun 2019 13:41:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (712 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。