Job ID = 1294590 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:08:00 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 ) 2019-06-03T00:08:00 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 ) 2019-06-03T00:08:00 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 ) 2019-06-03T00:08:00 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 ) 2019-06-03T00:11:13 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 : 22,382,823 reads read : 22,382,823 reads written : 22,382,823 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: 00:14:15 22382823 reads; of these: 22382823 (100.00%) were unpaired; of these: 1147799 (5.13%) aligned 0 times 14422309 (64.43%) aligned exactly 1 time 6812715 (30.44%) aligned >1 times 94.87% overall alignment rate Time searching: 00:14:15 Overall time: 00:14:15 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 12 files... [bam_rmdupse_core] 4905229 / 21235024 = 0.2310 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 09:42:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.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 09:42:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:42:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:42:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.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 09:42:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:42:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:42:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.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 09:42:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:42:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:43:05: 1000000 INFO @ Mon, 03 Jun 2019 09:43:05: 1000000 INFO @ Mon, 03 Jun 2019 09:43:06: 1000000 INFO @ Mon, 03 Jun 2019 09:43:18: 2000000 INFO @ Mon, 03 Jun 2019 09:43:19: 2000000 INFO @ Mon, 03 Jun 2019 09:43:21: 2000000 INFO @ Mon, 03 Jun 2019 09:43:31: 3000000 INFO @ Mon, 03 Jun 2019 09:43:32: 3000000 INFO @ Mon, 03 Jun 2019 09:43:36: 3000000 INFO @ Mon, 03 Jun 2019 09:43:43: 4000000 INFO @ Mon, 03 Jun 2019 09:43:46: 4000000 INFO @ Mon, 03 Jun 2019 09:43:51: 4000000 INFO @ Mon, 03 Jun 2019 09:43:56: 5000000 INFO @ Mon, 03 Jun 2019 09:43:59: 5000000 INFO @ Mon, 03 Jun 2019 09:44:06: 5000000 INFO @ Mon, 03 Jun 2019 09:44:09: 6000000 INFO @ Mon, 03 Jun 2019 09:44:12: 6000000 INFO @ Mon, 03 Jun 2019 09:44:20: 6000000 INFO @ Mon, 03 Jun 2019 09:44:21: 7000000 INFO @ Mon, 03 Jun 2019 09:44:26: 7000000 INFO @ Mon, 03 Jun 2019 09:44:32: 7000000 INFO @ Mon, 03 Jun 2019 09:44:33: 8000000 INFO @ Mon, 03 Jun 2019 09:44:41: 8000000 INFO @ Mon, 03 Jun 2019 09:44:46: 8000000 INFO @ Mon, 03 Jun 2019 09:44:46: 9000000 INFO @ Mon, 03 Jun 2019 09:44:55: 9000000 INFO @ Mon, 03 Jun 2019 09:44:58: 10000000 INFO @ Mon, 03 Jun 2019 09:44:59: 9000000 INFO @ Mon, 03 Jun 2019 09:45:09: 10000000 INFO @ Mon, 03 Jun 2019 09:45:10: 11000000 INFO @ Mon, 03 Jun 2019 09:45:12: 10000000 INFO @ Mon, 03 Jun 2019 09:45:22: 11000000 INFO @ Mon, 03 Jun 2019 09:45:23: 12000000 INFO @ Mon, 03 Jun 2019 09:45:25: 11000000 INFO @ Mon, 03 Jun 2019 09:45:35: 13000000 INFO @ Mon, 03 Jun 2019 09:45:35: 12000000 INFO @ Mon, 03 Jun 2019 09:45:38: 12000000 INFO @ Mon, 03 Jun 2019 09:45:48: 14000000 INFO @ Mon, 03 Jun 2019 09:45:49: 13000000 INFO @ Mon, 03 Jun 2019 09:45:52: 13000000 INFO @ Mon, 03 Jun 2019 09:46:01: 15000000 INFO @ Mon, 03 Jun 2019 09:46:02: 14000000 INFO @ Mon, 03 Jun 2019 09:46:06: 14000000 INFO @ Mon, 03 Jun 2019 09:46:15: 16000000 INFO @ Mon, 03 Jun 2019 09:46:15: 15000000 INFO @ Mon, 03 Jun 2019 09:46:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:46:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:46:19: #1 total tags in treatment: 16329795 INFO @ Mon, 03 Jun 2019 09:46:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:46:19: #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 09:46:19: 15000000 INFO @ Mon, 03 Jun 2019 09:46:19: #1 tags after filtering in treatment: 16329795 INFO @ Mon, 03 Jun 2019 09:46:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:46:19: #1 finished! INFO @ Mon, 03 Jun 2019 09:46:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:46:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:46:21: #2 number of paired peaks: 200 WARNING @ Mon, 03 Jun 2019 09:46:21: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 03 Jun 2019 09:46:21: start model_add_line... INFO @ Mon, 03 Jun 2019 09:46:21: start X-correlation... INFO @ Mon, 03 Jun 2019 09:46:21: end of X-cor INFO @ Mon, 03 Jun 2019 09:46:21: #2 finished! INFO @ Mon, 03 Jun 2019 09:46:21: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 09:46:21: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 09:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.05_model.r WARNING @ Mon, 03 Jun 2019 09:46:21: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:46:21: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 09:46:21: #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 09:46:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:46:27: 16000000 INFO @ Mon, 03 Jun 2019 09:46:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:46:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:46:31: #1 total tags in treatment: 16329795 INFO @ Mon, 03 Jun 2019 09:46:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:46:31: #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 09:46:32: 16000000 INFO @ Mon, 03 Jun 2019 09:46:32: #1 tags after filtering in treatment: 16329795 INFO @ Mon, 03 Jun 2019 09:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:46:32: #1 finished! INFO @ Mon, 03 Jun 2019 09:46:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:46:34: #2 number of paired peaks: 200 WARNING @ Mon, 03 Jun 2019 09:46:34: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 03 Jun 2019 09:46:34: start model_add_line... INFO @ Mon, 03 Jun 2019 09:46:34: start X-correlation... INFO @ Mon, 03 Jun 2019 09:46:34: end of X-cor INFO @ Mon, 03 Jun 2019 09:46:34: #2 finished! INFO @ Mon, 03 Jun 2019 09:46:34: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 09:46:34: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 09:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.10_model.r WARNING @ Mon, 03 Jun 2019 09:46:34: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:46:34: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 09:46:34: #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 09:46:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:46:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:46:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:46:36: #1 total tags in treatment: 16329795 INFO @ Mon, 03 Jun 2019 09:46:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:46:36: #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 09:46:36: #1 tags after filtering in treatment: 16329795 INFO @ Mon, 03 Jun 2019 09:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:46:36: #1 finished! INFO @ Mon, 03 Jun 2019 09:46:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:46:38: #2 number of paired peaks: 200 WARNING @ Mon, 03 Jun 2019 09:46:38: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Mon, 03 Jun 2019 09:46:38: start model_add_line... INFO @ Mon, 03 Jun 2019 09:46:38: start X-correlation... INFO @ Mon, 03 Jun 2019 09:46:38: end of X-cor INFO @ Mon, 03 Jun 2019 09:46:38: #2 finished! INFO @ Mon, 03 Jun 2019 09:46:38: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 09:46:38: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 09:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.20_model.r WARNING @ Mon, 03 Jun 2019 09:46:38: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:46:38: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 09:46:38: #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 09:46:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:47:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:47:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:47:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.05_summits.bed INFO @ Mon, 03 Jun 2019 09:47:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2198 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.10_summits.bed INFO @ Mon, 03 Jun 2019 09:47:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1808 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:48:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:48:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:48:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287763/SRX287763.20_summits.bed INFO @ Mon, 03 Jun 2019 09:48:03: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1299 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。