Job ID = 2640616 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:08:29 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 ) 2019-08-24T09:09:02 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 : 19,713,910 reads read : 39,427,820 reads written : 19,713,910 reads 0-length : 19,713,910 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:16:56 19713910 reads; of these: 19713910 (100.00%) were unpaired; of these: 1292279 (6.56%) aligned 0 times 13712721 (69.56%) aligned exactly 1 time 4708910 (23.89%) aligned >1 times 93.44% overall alignment rate Time searching: 00:16:59 Overall time: 00:16:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1103640 / 18421631 = 0.0599 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:35:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:35:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:35:11: 1000000 INFO @ Sat, 24 Aug 2019 18:35:18: 2000000 INFO @ Sat, 24 Aug 2019 18:35:25: 3000000 INFO @ Sat, 24 Aug 2019 18:35:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:35:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:35:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:35:33: 4000000 INFO @ Sat, 24 Aug 2019 18:35:43: 1000000 INFO @ Sat, 24 Aug 2019 18:35:43: 5000000 INFO @ Sat, 24 Aug 2019 18:35:58: 2000000 INFO @ Sat, 24 Aug 2019 18:35:58: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 18:36:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:36:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:36:10: 7000000 INFO @ Sat, 24 Aug 2019 18:36:10: 3000000 INFO @ Sat, 24 Aug 2019 18:36:14: 1000000 INFO @ Sat, 24 Aug 2019 18:36:18: 8000000 INFO @ Sat, 24 Aug 2019 18:36:20: 4000000 INFO @ Sat, 24 Aug 2019 18:36:24: 2000000 INFO @ Sat, 24 Aug 2019 18:36:25: 9000000 INFO @ Sat, 24 Aug 2019 18:36:28: 5000000 INFO @ Sat, 24 Aug 2019 18:36:36: 3000000 INFO @ Sat, 24 Aug 2019 18:36:36: 10000000 INFO @ Sat, 24 Aug 2019 18:36:40: 6000000 INFO @ Sat, 24 Aug 2019 18:36:45: 11000000 INFO @ Sat, 24 Aug 2019 18:36:45: 4000000 INFO @ Sat, 24 Aug 2019 18:36:48: 7000000 INFO @ Sat, 24 Aug 2019 18:36:52: 12000000 INFO @ Sat, 24 Aug 2019 18:36:54: 5000000 INFO @ Sat, 24 Aug 2019 18:36:56: 8000000 INFO @ Sat, 24 Aug 2019 18:37:00: 13000000 INFO @ Sat, 24 Aug 2019 18:37:02: 6000000 INFO @ Sat, 24 Aug 2019 18:37:03: 9000000 INFO @ Sat, 24 Aug 2019 18:37:07: 14000000 INFO @ Sat, 24 Aug 2019 18:37:11: 10000000 INFO @ Sat, 24 Aug 2019 18:37:12: 7000000 INFO @ Sat, 24 Aug 2019 18:37:15: 15000000 INFO @ Sat, 24 Aug 2019 18:37:19: 11000000 INFO @ Sat, 24 Aug 2019 18:37:21: 8000000 INFO @ Sat, 24 Aug 2019 18:37:22: 16000000 INFO @ Sat, 24 Aug 2019 18:37:27: 12000000 INFO @ Sat, 24 Aug 2019 18:37:30: 17000000 INFO @ Sat, 24 Aug 2019 18:37:31: 9000000 INFO @ Sat, 24 Aug 2019 18:37:33: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:37:33: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:37:33: #1 total tags in treatment: 17317991 INFO @ Sat, 24 Aug 2019 18:37:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:37:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:37:33: #1 tags after filtering in treatment: 17317800 INFO @ Sat, 24 Aug 2019 18:37:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:37:33: #1 finished! INFO @ Sat, 24 Aug 2019 18:37:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:37:35: 13000000 INFO @ Sat, 24 Aug 2019 18:37:35: #2 number of paired peaks: 7121 INFO @ Sat, 24 Aug 2019 18:37:35: start model_add_line... INFO @ Sat, 24 Aug 2019 18:37:36: start X-correlation... INFO @ Sat, 24 Aug 2019 18:37:36: end of X-cor INFO @ Sat, 24 Aug 2019 18:37:36: #2 finished! INFO @ Sat, 24 Aug 2019 18:37:36: #2 predicted fragment length is 59 bps INFO @ Sat, 24 Aug 2019 18:37:36: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 24 Aug 2019 18:37:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.05_model.r WARNING @ Sat, 24 Aug 2019 18:37:36: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:37:36: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 24 Aug 2019 18:37:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:37:36: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:37:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:37:40: 10000000 INFO @ Sat, 24 Aug 2019 18:37:43: 14000000 INFO @ Sat, 24 Aug 2019 18:37:50: 11000000 INFO @ Sat, 24 Aug 2019 18:37:51: 15000000 INFO @ Sat, 24 Aug 2019 18:37:59: 16000000 INFO @ Sat, 24 Aug 2019 18:37:59: 12000000 INFO @ Sat, 24 Aug 2019 18:38:07: 17000000 INFO @ Sat, 24 Aug 2019 18:38:09: 13000000 INFO @ Sat, 24 Aug 2019 18:38:09: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:38:09: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:38:09: #1 total tags in treatment: 17317991 INFO @ Sat, 24 Aug 2019 18:38:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:38:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:38:10: #1 tags after filtering in treatment: 17317800 INFO @ Sat, 24 Aug 2019 18:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:38:10: #1 finished! INFO @ Sat, 24 Aug 2019 18:38:10: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:38:12: #2 number of paired peaks: 7121 INFO @ Sat, 24 Aug 2019 18:38:12: start model_add_line... INFO @ Sat, 24 Aug 2019 18:38:12: start X-correlation... INFO @ Sat, 24 Aug 2019 18:38:12: end of X-cor INFO @ Sat, 24 Aug 2019 18:38:12: #2 finished! INFO @ Sat, 24 Aug 2019 18:38:12: #2 predicted fragment length is 59 bps INFO @ Sat, 24 Aug 2019 18:38:12: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 24 Aug 2019 18:38:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.10_model.r WARNING @ Sat, 24 Aug 2019 18:38:12: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:38:12: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 24 Aug 2019 18:38:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:38:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:38:18: 14000000 INFO @ Sat, 24 Aug 2019 18:38:27: 15000000 INFO @ Sat, 24 Aug 2019 18:38:29: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:38:36: 16000000 INFO @ Sat, 24 Aug 2019 18:38:45: 17000000 INFO @ Sat, 24 Aug 2019 18:38:48: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:38:48: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:38:48: #1 total tags in treatment: 17317991 INFO @ Sat, 24 Aug 2019 18:38:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:38:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:38:49: #1 tags after filtering in treatment: 17317800 INFO @ Sat, 24 Aug 2019 18:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:38:49: #1 finished! INFO @ Sat, 24 Aug 2019 18:38:49: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:38:51: #2 number of paired peaks: 7121 INFO @ Sat, 24 Aug 2019 18:38:51: start model_add_line... INFO @ Sat, 24 Aug 2019 18:38:51: start X-correlation... INFO @ Sat, 24 Aug 2019 18:38:51: end of X-cor INFO @ Sat, 24 Aug 2019 18:38:51: #2 finished! INFO @ Sat, 24 Aug 2019 18:38:51: #2 predicted fragment length is 59 bps INFO @ Sat, 24 Aug 2019 18:38:51: #2 alternative fragment length(s) may be 59 bps INFO @ Sat, 24 Aug 2019 18:38:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.20_model.r WARNING @ Sat, 24 Aug 2019 18:38:51: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:38:51: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sat, 24 Aug 2019 18:38:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 18:38:51: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:38:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:38:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:38:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:38:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.05_summits.bed INFO @ Sat, 24 Aug 2019 18:38:56: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (1704 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:39:06: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:39:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:39:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:39:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.10_summits.bed INFO @ Sat, 24 Aug 2019 18:39:35: Done! pass1 - making usageList (32 chroms): 3 millis pass2 - checking and writing primary data (757 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:39:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:40:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:40:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:40:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375039/SRX5375039.20_summits.bed INFO @ Sat, 24 Aug 2019 18:40:16: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (299 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。