Job ID = 4288962 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,973,143 reads read : 21,946,286 reads written : 10,973,143 reads 0-length : 10,973,143 2019-12-10T04:39:55 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 ) 2019-12-10T04:39:55 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 : 13,033,869 reads read : 26,067,738 reads written : 13,033,869 reads 0-length : 13,033,869 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:07 24007012 reads; of these: 24007012 (100.00%) were unpaired; of these: 4598452 (19.15%) aligned 0 times 15624682 (65.08%) aligned exactly 1 time 3783878 (15.76%) aligned >1 times 80.85% overall alignment rate Time searching: 00:29:09 Overall time: 00:29:09 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] 2140372 / 19408560 = 0.1103 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.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 14:23:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:23:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:23:32: 1000000 INFO @ Tue, 10 Dec 2019 14:23:45: 2000000 INFO @ Tue, 10 Dec 2019 14:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.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 14:23:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:23:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:23:57: 3000000 INFO @ Tue, 10 Dec 2019 14:24:03: 1000000 INFO @ Tue, 10 Dec 2019 14:24:10: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:24:17: 2000000 INFO @ Tue, 10 Dec 2019 14:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.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 14:24:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:24:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:24:23: 5000000 INFO @ Tue, 10 Dec 2019 14:24:31: 3000000 INFO @ Tue, 10 Dec 2019 14:24:33: 1000000 INFO @ Tue, 10 Dec 2019 14:24:35: 6000000 INFO @ Tue, 10 Dec 2019 14:24:45: 4000000 INFO @ Tue, 10 Dec 2019 14:24:46: 7000000 INFO @ Tue, 10 Dec 2019 14:24:48: 2000000 INFO @ Tue, 10 Dec 2019 14:24:57: 8000000 INFO @ Tue, 10 Dec 2019 14:24:59: 5000000 INFO @ Tue, 10 Dec 2019 14:25:02: 3000000 INFO @ Tue, 10 Dec 2019 14:25:08: 9000000 INFO @ Tue, 10 Dec 2019 14:25:13: 6000000 INFO @ Tue, 10 Dec 2019 14:25:16: 4000000 INFO @ Tue, 10 Dec 2019 14:25:19: 10000000 INFO @ Tue, 10 Dec 2019 14:25:28: 7000000 INFO @ Tue, 10 Dec 2019 14:25:29: 5000000 INFO @ Tue, 10 Dec 2019 14:25:31: 11000000 INFO @ Tue, 10 Dec 2019 14:25:42: 8000000 INFO @ Tue, 10 Dec 2019 14:25:43: 12000000 INFO @ Tue, 10 Dec 2019 14:25:44: 6000000 INFO @ Tue, 10 Dec 2019 14:25:53: 13000000 INFO @ Tue, 10 Dec 2019 14:25:57: 9000000 INFO @ Tue, 10 Dec 2019 14:25:59: 7000000 INFO @ Tue, 10 Dec 2019 14:26:03: 14000000 INFO @ Tue, 10 Dec 2019 14:26:12: 10000000 INFO @ Tue, 10 Dec 2019 14:26:14: 15000000 INFO @ Tue, 10 Dec 2019 14:26:15: 8000000 INFO @ Tue, 10 Dec 2019 14:26:27: 16000000 INFO @ Tue, 10 Dec 2019 14:26:28: 11000000 INFO @ Tue, 10 Dec 2019 14:26:30: 9000000 INFO @ Tue, 10 Dec 2019 14:26:39: 17000000 INFO @ Tue, 10 Dec 2019 14:26:43: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 14:26:43: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 14:26:43: #1 total tags in treatment: 17268188 INFO @ Tue, 10 Dec 2019 14:26:43: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:26:43: #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 14:26:43: 12000000 INFO @ Tue, 10 Dec 2019 14:26:43: #1 tags after filtering in treatment: 17268011 INFO @ Tue, 10 Dec 2019 14:26:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:26:43: #1 finished! INFO @ Tue, 10 Dec 2019 14:26:43: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:26:45: 10000000 INFO @ Tue, 10 Dec 2019 14:26:47: #2 number of paired peaks: 36083 INFO @ Tue, 10 Dec 2019 14:26:47: start model_add_line... INFO @ Tue, 10 Dec 2019 14:26:48: start X-correlation... INFO @ Tue, 10 Dec 2019 14:26:48: end of X-cor INFO @ Tue, 10 Dec 2019 14:26:48: #2 finished! INFO @ Tue, 10 Dec 2019 14:26:48: #2 predicted fragment length is 139 bps INFO @ Tue, 10 Dec 2019 14:26:48: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 10 Dec 2019 14:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.05_model.r WARNING @ Tue, 10 Dec 2019 14:26:48: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:26:48: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 10 Dec 2019 14:26:48: #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 14:26:48: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:26:58: 13000000 INFO @ Tue, 10 Dec 2019 14:27:00: 11000000 INFO @ Tue, 10 Dec 2019 14:27:11: 14000000 INFO @ Tue, 10 Dec 2019 14:27:15: 12000000 INFO @ Tue, 10 Dec 2019 14:27:25: 15000000 INFO @ Tue, 10 Dec 2019 14:27:29: 13000000 INFO @ Tue, 10 Dec 2019 14:27:39: 16000000 INFO @ Tue, 10 Dec 2019 14:27:43: 14000000 INFO @ Tue, 10 Dec 2019 14:27:53: 17000000 INFO @ Tue, 10 Dec 2019 14:27:57: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 14:27:57: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 14:27:57: #1 total tags in treatment: 17268188 INFO @ Tue, 10 Dec 2019 14:27:57: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:27:57: #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 14:27:57: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:27:57: #1 tags after filtering in treatment: 17268011 INFO @ Tue, 10 Dec 2019 14:27:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:27:57: #1 finished! INFO @ Tue, 10 Dec 2019 14:27:57: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:27:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:27:57: 15000000 INFO @ Tue, 10 Dec 2019 14:28:01: #2 number of paired peaks: 36083 INFO @ Tue, 10 Dec 2019 14:28:01: start model_add_line... INFO @ Tue, 10 Dec 2019 14:28:02: start X-correlation... INFO @ Tue, 10 Dec 2019 14:28:02: end of X-cor INFO @ Tue, 10 Dec 2019 14:28:02: #2 finished! INFO @ Tue, 10 Dec 2019 14:28:02: #2 predicted fragment length is 139 bps INFO @ Tue, 10 Dec 2019 14:28:02: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 10 Dec 2019 14:28:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.10_model.r WARNING @ Tue, 10 Dec 2019 14:28:02: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:28:02: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 10 Dec 2019 14:28:02: #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 14:28:02: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:28:11: 16000000 INFO @ Tue, 10 Dec 2019 14:28:23: 17000000 INFO @ Tue, 10 Dec 2019 14:28:27: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 14:28:27: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 14:28:27: #1 total tags in treatment: 17268188 INFO @ Tue, 10 Dec 2019 14:28:27: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:28:27: #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 14:28:27: #1 tags after filtering in treatment: 17268011 INFO @ Tue, 10 Dec 2019 14:28:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:28:27: #1 finished! INFO @ Tue, 10 Dec 2019 14:28:27: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:28:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:28:31: #2 number of paired peaks: 36083 INFO @ Tue, 10 Dec 2019 14:28:31: start model_add_line... INFO @ Tue, 10 Dec 2019 14:28:31: start X-correlation... INFO @ Tue, 10 Dec 2019 14:28:31: end of X-cor INFO @ Tue, 10 Dec 2019 14:28:31: #2 finished! INFO @ Tue, 10 Dec 2019 14:28:31: #2 predicted fragment length is 139 bps INFO @ Tue, 10 Dec 2019 14:28:31: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 10 Dec 2019 14:28:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.20_model.r WARNING @ Tue, 10 Dec 2019 14:28:31: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:28:31: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 10 Dec 2019 14:28:31: #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 14:28:31: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:28:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.05_summits.bed INFO @ Tue, 10 Dec 2019 14:28:35: Done! pass1 - making usageList (61 chroms): 3 millis pass2 - checking and writing primary data (7694 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:29:06: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:29:32: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.10_summits.bed INFO @ Tue, 10 Dec 2019 14:29:37: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (3371 records, 4 fields): 81 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:30:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:30:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:30:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460582/SRX5460582.20_summits.bed INFO @ Tue, 10 Dec 2019 14:30:00: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (891 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。