Job ID = 4288945 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:51:16 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 : 7,116,566 reads read : 14,233,132 reads written : 7,116,566 reads 0-length : 7,116,566 2019-12-10T03:55:55 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 : 9,311,839 reads read : 18,623,678 reads written : 9,311,839 reads 0-length : 9,311,839 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:23 16428405 reads; of these: 16428405 (100.00%) were unpaired; of these: 1367495 (8.32%) aligned 0 times 11625496 (70.76%) aligned exactly 1 time 3435414 (20.91%) aligned >1 times 91.68% overall alignment rate Time searching: 00:16:25 Overall time: 00:16:25 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] 4243300 / 15060910 = 0.2817 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.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 13:24:57: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:24:57: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:25:08: 1000000 INFO @ Tue, 10 Dec 2019 13:25:19: 2000000 INFO @ Tue, 10 Dec 2019 13:25:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.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 13:25:26: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:25:26: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:25:29: 3000000 INFO @ Tue, 10 Dec 2019 13:25:37: 1000000 INFO @ Tue, 10 Dec 2019 13:25:40: 4000000 INFO @ Tue, 10 Dec 2019 13:25:46: 2000000 INFO @ Tue, 10 Dec 2019 13:25:51: 5000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:25:55: 3000000 INFO @ Tue, 10 Dec 2019 13:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.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 13:25:56: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:25:56: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:26:02: 6000000 INFO @ Tue, 10 Dec 2019 13:26:04: 4000000 INFO @ Tue, 10 Dec 2019 13:26:06: 1000000 INFO @ Tue, 10 Dec 2019 13:26:13: 7000000 INFO @ Tue, 10 Dec 2019 13:26:14: 5000000 INFO @ Tue, 10 Dec 2019 13:26:15: 2000000 INFO @ Tue, 10 Dec 2019 13:26:23: 8000000 INFO @ Tue, 10 Dec 2019 13:26:24: 3000000 INFO @ Tue, 10 Dec 2019 13:26:25: 6000000 INFO @ Tue, 10 Dec 2019 13:26:32: 4000000 INFO @ Tue, 10 Dec 2019 13:26:34: 9000000 INFO @ Tue, 10 Dec 2019 13:26:35: 7000000 INFO @ Tue, 10 Dec 2019 13:26:41: 5000000 INFO @ Tue, 10 Dec 2019 13:26:44: 10000000 INFO @ Tue, 10 Dec 2019 13:26:46: 8000000 INFO @ Tue, 10 Dec 2019 13:26:50: 6000000 INFO @ Tue, 10 Dec 2019 13:26:53: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:26:53: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:26:53: #1 total tags in treatment: 10817610 INFO @ Tue, 10 Dec 2019 13:26:53: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:26:53: #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 13:26:54: #1 tags after filtering in treatment: 10817420 INFO @ Tue, 10 Dec 2019 13:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:26:54: #1 finished! INFO @ Tue, 10 Dec 2019 13:26:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:26:56: #2 number of paired peaks: 26842 INFO @ Tue, 10 Dec 2019 13:26:56: start model_add_line... INFO @ Tue, 10 Dec 2019 13:26:56: 9000000 INFO @ Tue, 10 Dec 2019 13:26:56: start X-correlation... INFO @ Tue, 10 Dec 2019 13:26:56: end of X-cor INFO @ Tue, 10 Dec 2019 13:26:56: #2 finished! INFO @ Tue, 10 Dec 2019 13:26:56: #2 predicted fragment length is 159 bps INFO @ Tue, 10 Dec 2019 13:26:56: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 10 Dec 2019 13:26:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.05_model.r WARNING @ Tue, 10 Dec 2019 13:26:56: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:26:56: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Tue, 10 Dec 2019 13:26:56: #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 13:26:56: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:26:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:26:59: 7000000 INFO @ Tue, 10 Dec 2019 13:27:06: 10000000 INFO @ Tue, 10 Dec 2019 13:27:07: 8000000 INFO @ Tue, 10 Dec 2019 13:27:14: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:27:14: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:27:14: #1 total tags in treatment: 10817610 INFO @ Tue, 10 Dec 2019 13:27:14: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:27:14: #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 13:27:15: #1 tags after filtering in treatment: 10817420 INFO @ Tue, 10 Dec 2019 13:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:27:15: #1 finished! INFO @ Tue, 10 Dec 2019 13:27:15: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:27:16: 9000000 INFO @ Tue, 10 Dec 2019 13:27:17: #2 number of paired peaks: 26842 INFO @ Tue, 10 Dec 2019 13:27:17: start model_add_line... INFO @ Tue, 10 Dec 2019 13:27:17: start X-correlation... INFO @ Tue, 10 Dec 2019 13:27:17: end of X-cor INFO @ Tue, 10 Dec 2019 13:27:17: #2 finished! INFO @ Tue, 10 Dec 2019 13:27:17: #2 predicted fragment length is 159 bps INFO @ Tue, 10 Dec 2019 13:27:17: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 10 Dec 2019 13:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.10_model.r WARNING @ Tue, 10 Dec 2019 13:27:17: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:27:17: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Tue, 10 Dec 2019 13:27:17: #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 13:27:17: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:27:24: 10000000 INFO @ Tue, 10 Dec 2019 13:27:31: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:27:31: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:27:31: #1 total tags in treatment: 10817610 INFO @ Tue, 10 Dec 2019 13:27:31: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:27:31: #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 13:27:31: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:27:32: #1 tags after filtering in treatment: 10817420 INFO @ Tue, 10 Dec 2019 13:27:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:27:32: #1 finished! INFO @ Tue, 10 Dec 2019 13:27:32: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:27:34: #2 number of paired peaks: 26842 INFO @ Tue, 10 Dec 2019 13:27:34: start model_add_line... INFO @ Tue, 10 Dec 2019 13:27:34: start X-correlation... INFO @ Tue, 10 Dec 2019 13:27:34: end of X-cor INFO @ Tue, 10 Dec 2019 13:27:34: #2 finished! INFO @ Tue, 10 Dec 2019 13:27:34: #2 predicted fragment length is 159 bps INFO @ Tue, 10 Dec 2019 13:27:34: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 10 Dec 2019 13:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.20_model.r WARNING @ Tue, 10 Dec 2019 13:27:34: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:27:34: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Tue, 10 Dec 2019 13:27:34: #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 13:27:34: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:27:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:27:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:27:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.05_summits.bed INFO @ Tue, 10 Dec 2019 13:27:49: Done! pass1 - making usageList (68 chroms): 6 millis pass2 - checking and writing primary data (12698 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:27:53: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:28:09: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:28:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:28:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:28:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.10_summits.bed INFO @ Tue, 10 Dec 2019 13:28:10: Done! pass1 - making usageList (47 chroms): 3 millis pass2 - checking and writing primary data (5489 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460574/SRX5460574.20_summits.bed INFO @ Tue, 10 Dec 2019 13:28:27: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (1737 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。