Job ID = 4288930 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,253,143 reads read : 18,506,286 reads written : 9,253,143 reads 0-length : 9,253,143 2019-12-10T03:49:33 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 : 23,468,939 reads read : 46,937,878 reads written : 23,468,939 reads 0-length : 23,468,939 spots read : 3,641,348 reads read : 7,282,696 reads written : 3,641,348 reads 0-length : 3,641,348 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: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:47:47 36363430 reads; of these: 36363430 (100.00%) were unpaired; of these: 5571249 (15.32%) aligned 0 times 23964224 (65.90%) aligned exactly 1 time 6827957 (18.78%) aligned >1 times 84.68% overall alignment rate Time searching: 00:47:53 Overall time: 00:47:53 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 16 files... [bam_rmdupse_core] 6381788 / 30792181 = 0.2073 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.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 14:06:26: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:06:26: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:06:37: 1000000 INFO @ Tue, 10 Dec 2019 14:06:48: 2000000 INFO @ Tue, 10 Dec 2019 14:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.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 14:06:55: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:06:55: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:06:58: 3000000 INFO @ Tue, 10 Dec 2019 14:07:04: 1000000 INFO @ Tue, 10 Dec 2019 14:07:09: 4000000 INFO @ Tue, 10 Dec 2019 14:07:12: 2000000 INFO @ Tue, 10 Dec 2019 14:07:19: 5000000 INFO @ Tue, 10 Dec 2019 14:07:20: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:07:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.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 14:07:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:07:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:07:28: 4000000 INFO @ Tue, 10 Dec 2019 14:07:30: 6000000 INFO @ Tue, 10 Dec 2019 14:07:35: 1000000 INFO @ Tue, 10 Dec 2019 14:07:37: 5000000 INFO @ Tue, 10 Dec 2019 14:07:41: 7000000 INFO @ Tue, 10 Dec 2019 14:07:45: 2000000 INFO @ Tue, 10 Dec 2019 14:07:45: 6000000 INFO @ Tue, 10 Dec 2019 14:07:51: 8000000 INFO @ Tue, 10 Dec 2019 14:07:54: 7000000 INFO @ Tue, 10 Dec 2019 14:07:54: 3000000 INFO @ Tue, 10 Dec 2019 14:08:02: 9000000 INFO @ Tue, 10 Dec 2019 14:08:02: 8000000 INFO @ Tue, 10 Dec 2019 14:08:04: 4000000 INFO @ Tue, 10 Dec 2019 14:08:10: 9000000 INFO @ Tue, 10 Dec 2019 14:08:12: 10000000 INFO @ Tue, 10 Dec 2019 14:08:13: 5000000 INFO @ Tue, 10 Dec 2019 14:08:18: 10000000 INFO @ Tue, 10 Dec 2019 14:08:22: 6000000 INFO @ Tue, 10 Dec 2019 14:08:23: 11000000 INFO @ Tue, 10 Dec 2019 14:08:27: 11000000 INFO @ Tue, 10 Dec 2019 14:08:32: 7000000 INFO @ Tue, 10 Dec 2019 14:08:34: 12000000 INFO @ Tue, 10 Dec 2019 14:08:35: 12000000 INFO @ Tue, 10 Dec 2019 14:08:41: 8000000 INFO @ Tue, 10 Dec 2019 14:08:44: 13000000 INFO @ Tue, 10 Dec 2019 14:08:45: 13000000 INFO @ Tue, 10 Dec 2019 14:08:51: 9000000 INFO @ Tue, 10 Dec 2019 14:08:52: 14000000 INFO @ Tue, 10 Dec 2019 14:08:55: 14000000 INFO @ Tue, 10 Dec 2019 14:09:00: 10000000 INFO @ Tue, 10 Dec 2019 14:09:01: 15000000 INFO @ Tue, 10 Dec 2019 14:09:06: 15000000 INFO @ Tue, 10 Dec 2019 14:09:09: 16000000 INFO @ Tue, 10 Dec 2019 14:09:09: 11000000 INFO @ Tue, 10 Dec 2019 14:09:16: 16000000 INFO @ Tue, 10 Dec 2019 14:09:17: 17000000 INFO @ Tue, 10 Dec 2019 14:09:19: 12000000 INFO @ Tue, 10 Dec 2019 14:09:26: 18000000 INFO @ Tue, 10 Dec 2019 14:09:27: 17000000 INFO @ Tue, 10 Dec 2019 14:09:28: 13000000 INFO @ Tue, 10 Dec 2019 14:09:34: 19000000 INFO @ Tue, 10 Dec 2019 14:09:38: 14000000 INFO @ Tue, 10 Dec 2019 14:09:38: 18000000 INFO @ Tue, 10 Dec 2019 14:09:43: 20000000 INFO @ Tue, 10 Dec 2019 14:09:47: 15000000 INFO @ Tue, 10 Dec 2019 14:09:49: 19000000 INFO @ Tue, 10 Dec 2019 14:09:51: 21000000 INFO @ Tue, 10 Dec 2019 14:09:57: 16000000 INFO @ Tue, 10 Dec 2019 14:09:59: 20000000 INFO @ Tue, 10 Dec 2019 14:10:00: 22000000 INFO @ Tue, 10 Dec 2019 14:10:06: 17000000 INFO @ Tue, 10 Dec 2019 14:10:08: 23000000 INFO @ Tue, 10 Dec 2019 14:10:10: 21000000 INFO @ Tue, 10 Dec 2019 14:10:16: 18000000 INFO @ Tue, 10 Dec 2019 14:10:16: 24000000 INFO @ Tue, 10 Dec 2019 14:10:20: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 14:10:20: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 14:10:20: #1 total tags in treatment: 24410393 INFO @ Tue, 10 Dec 2019 14:10:20: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:10:20: #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 14:10:21: 22000000 INFO @ Tue, 10 Dec 2019 14:10:21: #1 tags after filtering in treatment: 24410281 INFO @ Tue, 10 Dec 2019 14:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:10:21: #1 finished! INFO @ Tue, 10 Dec 2019 14:10:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:10:24: #2 number of paired peaks: 15521 INFO @ Tue, 10 Dec 2019 14:10:24: start model_add_line... INFO @ Tue, 10 Dec 2019 14:10:24: start X-correlation... INFO @ Tue, 10 Dec 2019 14:10:24: end of X-cor INFO @ Tue, 10 Dec 2019 14:10:24: #2 finished! INFO @ Tue, 10 Dec 2019 14:10:24: #2 predicted fragment length is 144 bps INFO @ Tue, 10 Dec 2019 14:10:24: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 10 Dec 2019 14:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.10_model.r WARNING @ Tue, 10 Dec 2019 14:10:24: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:10:24: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 10 Dec 2019 14:10:24: #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 14:10:24: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:10:25: 19000000 INFO @ Tue, 10 Dec 2019 14:10:31: 23000000 INFO @ Tue, 10 Dec 2019 14:10:35: 20000000 INFO @ Tue, 10 Dec 2019 14:10:42: 24000000 INFO @ Tue, 10 Dec 2019 14:10:44: 21000000 INFO @ Tue, 10 Dec 2019 14:10:47: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 14:10:47: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 14:10:47: #1 total tags in treatment: 24410393 INFO @ Tue, 10 Dec 2019 14:10:47: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:10:47: #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 14:10:48: #1 tags after filtering in treatment: 24410281 INFO @ Tue, 10 Dec 2019 14:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:10:48: #1 finished! INFO @ Tue, 10 Dec 2019 14:10:48: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:10:51: #2 number of paired peaks: 15521 INFO @ Tue, 10 Dec 2019 14:10:51: start model_add_line... INFO @ Tue, 10 Dec 2019 14:10:51: start X-correlation... INFO @ Tue, 10 Dec 2019 14:10:51: end of X-cor INFO @ Tue, 10 Dec 2019 14:10:51: #2 finished! INFO @ Tue, 10 Dec 2019 14:10:51: #2 predicted fragment length is 144 bps INFO @ Tue, 10 Dec 2019 14:10:51: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 10 Dec 2019 14:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.05_model.r WARNING @ Tue, 10 Dec 2019 14:10:51: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:10:51: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 10 Dec 2019 14:10:51: #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 14:10:51: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:10:54: 22000000 INFO @ Tue, 10 Dec 2019 14:11:03: 23000000 INFO @ Tue, 10 Dec 2019 14:11:12: 24000000 INFO @ Tue, 10 Dec 2019 14:11:16: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 14:11:16: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 14:11:16: #1 total tags in treatment: 24410393 INFO @ Tue, 10 Dec 2019 14:11:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:11:16: #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 14:11:17: #1 tags after filtering in treatment: 24410281 INFO @ Tue, 10 Dec 2019 14:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:11:17: #1 finished! INFO @ Tue, 10 Dec 2019 14:11:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:11:20: #2 number of paired peaks: 15521 INFO @ Tue, 10 Dec 2019 14:11:20: start model_add_line... INFO @ Tue, 10 Dec 2019 14:11:20: start X-correlation... INFO @ Tue, 10 Dec 2019 14:11:20: end of X-cor INFO @ Tue, 10 Dec 2019 14:11:20: #2 finished! INFO @ Tue, 10 Dec 2019 14:11:20: #2 predicted fragment length is 144 bps INFO @ Tue, 10 Dec 2019 14:11:20: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 10 Dec 2019 14:11:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.20_model.r WARNING @ Tue, 10 Dec 2019 14:11:20: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 14:11:20: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 10 Dec 2019 14:11:20: #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 14:11:20: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:11:41: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:12:08: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.10_summits.bed INFO @ Tue, 10 Dec 2019 14:12:22: Done! pass1 - making usageList (49 chroms): 4 millis pass2 - checking and writing primary data (5542 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:12:39: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:12:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:12:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:12:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.05_summits.bed INFO @ Tue, 10 Dec 2019 14:12:49: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (13742 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460568/SRX5460568.20_summits.bed INFO @ Tue, 10 Dec 2019 14:13:21: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (1632 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。