Job ID = 4288932 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:46:20 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-10T03:49:06 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 ) 2019-12-10T03:49:06 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 : 18,365,024 reads read : 36,730,048 reads written : 18,365,024 reads 0-length : 18,365,024 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:27:40 18365024 reads; of these: 18365024 (100.00%) were unpaired; of these: 3431385 (18.68%) aligned 0 times 11711540 (63.77%) aligned exactly 1 time 3222099 (17.54%) aligned >1 times 81.32% overall alignment rate Time searching: 00:27:42 Overall time: 00:27:42 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] 2477601 / 14933639 = 0.1659 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.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 @ Tue, 10 Dec 2019 13:28:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:28:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:28:12: 1000000 INFO @ Tue, 10 Dec 2019 13:28:20: 2000000 INFO @ Tue, 10 Dec 2019 13:28:28: 3000000 INFO @ Tue, 10 Dec 2019 13:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.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 @ Tue, 10 Dec 2019 13:28:34: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:28:34: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:28:36: 4000000 INFO @ Tue, 10 Dec 2019 13:28:45: 5000000 INFO @ Tue, 10 Dec 2019 13:28:46: 1000000 INFO @ Tue, 10 Dec 2019 13:28:53: 6000000 INFO @ Tue, 10 Dec 2019 13:28:57: 2000000 INFO @ Tue, 10 Dec 2019 13:29:01: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.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 @ Tue, 10 Dec 2019 13:29:04: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:29:04: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:29:08: 3000000 INFO @ Tue, 10 Dec 2019 13:29:09: 8000000 INFO @ Tue, 10 Dec 2019 13:29:14: 1000000 INFO @ Tue, 10 Dec 2019 13:29:17: 9000000 INFO @ Tue, 10 Dec 2019 13:29:20: 4000000 INFO @ Tue, 10 Dec 2019 13:29:23: 2000000 INFO @ Tue, 10 Dec 2019 13:29:26: 10000000 INFO @ Tue, 10 Dec 2019 13:29:32: 3000000 INFO @ Tue, 10 Dec 2019 13:29:32: 5000000 INFO @ Tue, 10 Dec 2019 13:29:35: 11000000 INFO @ Tue, 10 Dec 2019 13:29:41: 4000000 INFO @ Tue, 10 Dec 2019 13:29:43: 6000000 INFO @ Tue, 10 Dec 2019 13:29:45: 12000000 INFO @ Tue, 10 Dec 2019 13:29:49: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:29:49: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:29:49: #1 total tags in treatment: 12456038 INFO @ Tue, 10 Dec 2019 13:29:49: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:29:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:29:49: #1 tags after filtering in treatment: 12455865 INFO @ Tue, 10 Dec 2019 13:29:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:29:49: #1 finished! INFO @ Tue, 10 Dec 2019 13:29:49: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:29:50: 5000000 INFO @ Tue, 10 Dec 2019 13:29:52: #2 number of paired peaks: 23917 INFO @ Tue, 10 Dec 2019 13:29:52: start model_add_line... INFO @ Tue, 10 Dec 2019 13:29:52: start X-correlation... INFO @ Tue, 10 Dec 2019 13:29:52: end of X-cor INFO @ Tue, 10 Dec 2019 13:29:52: #2 finished! INFO @ Tue, 10 Dec 2019 13:29:52: #2 predicted fragment length is 155 bps INFO @ Tue, 10 Dec 2019 13:29:52: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 10 Dec 2019 13:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.05_model.r WARNING @ Tue, 10 Dec 2019 13:29:52: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:29:52: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Tue, 10 Dec 2019 13:29:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:29:52: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:29:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:29:54: 7000000 INFO @ Tue, 10 Dec 2019 13:29:59: 6000000 INFO @ Tue, 10 Dec 2019 13:30:06: 8000000 INFO @ Tue, 10 Dec 2019 13:30:08: 7000000 INFO @ Tue, 10 Dec 2019 13:30:16: 9000000 INFO @ Tue, 10 Dec 2019 13:30:17: 8000000 INFO @ Tue, 10 Dec 2019 13:30:25: 9000000 INFO @ Tue, 10 Dec 2019 13:30:28: 10000000 INFO @ Tue, 10 Dec 2019 13:30:32: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:30:34: 10000000 INFO @ Tue, 10 Dec 2019 13:30:40: 11000000 INFO @ Tue, 10 Dec 2019 13:30:44: 11000000 INFO @ Tue, 10 Dec 2019 13:30:52: 12000000 INFO @ Tue, 10 Dec 2019 13:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:30:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:30:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.05_summits.bed INFO @ Tue, 10 Dec 2019 13:30:53: Done! INFO @ Tue, 10 Dec 2019 13:30:53: 12000000 pass1 - making usageList (68 chroms): 6 millis pass2 - checking and writing primary data (12012 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:30:57: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:30:57: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:30:57: #1 total tags in treatment: 12456038 INFO @ Tue, 10 Dec 2019 13:30:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:30:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:30:58: #1 tags after filtering in treatment: 12455865 INFO @ Tue, 10 Dec 2019 13:30:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:30:58: #1 finished! INFO @ Tue, 10 Dec 2019 13:30:58: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:30:58: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:30:58: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:30:58: #1 total tags in treatment: 12456038 INFO @ Tue, 10 Dec 2019 13:30:58: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:30:58: #1 tags after filtering in treatment: 12455865 INFO @ Tue, 10 Dec 2019 13:30:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:30:58: #1 finished! INFO @ Tue, 10 Dec 2019 13:30:58: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:31:00: #2 number of paired peaks: 23917 INFO @ Tue, 10 Dec 2019 13:31:00: start model_add_line... INFO @ Tue, 10 Dec 2019 13:31:00: start X-correlation... INFO @ Tue, 10 Dec 2019 13:31:00: end of X-cor INFO @ Tue, 10 Dec 2019 13:31:00: #2 finished! INFO @ Tue, 10 Dec 2019 13:31:00: #2 predicted fragment length is 155 bps INFO @ Tue, 10 Dec 2019 13:31:00: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 10 Dec 2019 13:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.20_model.r WARNING @ Tue, 10 Dec 2019 13:31:00: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:31:00: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Tue, 10 Dec 2019 13:31:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:31:00: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:31:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:31:01: #2 number of paired peaks: 23917 INFO @ Tue, 10 Dec 2019 13:31:01: start model_add_line... INFO @ Tue, 10 Dec 2019 13:31:01: start X-correlation... INFO @ Tue, 10 Dec 2019 13:31:01: end of X-cor INFO @ Tue, 10 Dec 2019 13:31:01: #2 finished! INFO @ Tue, 10 Dec 2019 13:31:01: #2 predicted fragment length is 155 bps INFO @ Tue, 10 Dec 2019 13:31:01: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 10 Dec 2019 13:31:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.10_model.r WARNING @ Tue, 10 Dec 2019 13:31:01: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:31:01: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Tue, 10 Dec 2019 13:31:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:31:01: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:31:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:31:41: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:31:41: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.20_summits.bed INFO @ Tue, 10 Dec 2019 13:32:00: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (1111 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:32:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:32:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:32:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460569/SRX5460569.10_summits.bed INFO @ Tue, 10 Dec 2019 13:32:01: Done! pass1 - making usageList (44 chroms): 4 millis pass2 - checking and writing primary data (4357 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。