Job ID = 2640734 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T09:53:40 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 ) 2019-08-24T09:53:40 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 ) 2019-08-24T09:53:40 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 ) 2019-08-24T09:57:14 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 ) 2019-08-24T10:07:45 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 ) 2019-08-24T10:07:45 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 : 38,164,305 reads read : 38,164,305 reads written : 38,164,305 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:14:01 38164305 reads; of these: 38164305 (100.00%) were unpaired; of these: 2177966 (5.71%) aligned 0 times 26360293 (69.07%) aligned exactly 1 time 9626046 (25.22%) aligned >1 times 94.29% overall alignment rate Time searching: 01:14:05 Overall time: 01:14:05 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] 2990940 / 35986339 = 0.0831 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:02:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.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 21:02:20: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:02:20: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:02:30: 1000000 INFO @ Sat, 24 Aug 2019 21:02:40: 2000000 INFO @ Sat, 24 Aug 2019 21:02:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.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 21:02:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:02:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:02:50: 3000000 INFO @ Sat, 24 Aug 2019 21:03:01: 4000000 INFO @ Sat, 24 Aug 2019 21:03:03: 1000000 INFO @ Sat, 24 Aug 2019 21:03:12: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:03:17: 2000000 INFO @ Sat, 24 Aug 2019 21:03:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.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 21:03:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:03:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:03:24: 6000000 INFO @ Sat, 24 Aug 2019 21:03:31: 1000000 INFO @ Sat, 24 Aug 2019 21:03:32: 3000000 INFO @ Sat, 24 Aug 2019 21:03:35: 7000000 INFO @ Sat, 24 Aug 2019 21:03:44: 2000000 INFO @ Sat, 24 Aug 2019 21:03:46: 8000000 INFO @ Sat, 24 Aug 2019 21:03:47: 4000000 INFO @ Sat, 24 Aug 2019 21:03:57: 3000000 INFO @ Sat, 24 Aug 2019 21:03:57: 9000000 INFO @ Sat, 24 Aug 2019 21:04:01: 5000000 INFO @ Sat, 24 Aug 2019 21:04:08: 10000000 INFO @ Sat, 24 Aug 2019 21:04:09: 4000000 INFO @ Sat, 24 Aug 2019 21:04:16: 6000000 INFO @ Sat, 24 Aug 2019 21:04:19: 11000000 INFO @ Sat, 24 Aug 2019 21:04:21: 5000000 INFO @ Sat, 24 Aug 2019 21:04:30: 12000000 INFO @ Sat, 24 Aug 2019 21:04:30: 7000000 INFO @ Sat, 24 Aug 2019 21:04:34: 6000000 INFO @ Sat, 24 Aug 2019 21:04:41: 13000000 INFO @ Sat, 24 Aug 2019 21:04:44: 8000000 INFO @ Sat, 24 Aug 2019 21:04:47: 7000000 INFO @ Sat, 24 Aug 2019 21:04:51: 14000000 INFO @ Sat, 24 Aug 2019 21:04:59: 8000000 INFO @ Sat, 24 Aug 2019 21:04:59: 9000000 INFO @ Sat, 24 Aug 2019 21:05:02: 15000000 INFO @ Sat, 24 Aug 2019 21:05:11: 9000000 INFO @ Sat, 24 Aug 2019 21:05:13: 16000000 INFO @ Sat, 24 Aug 2019 21:05:15: 10000000 INFO @ Sat, 24 Aug 2019 21:05:24: 10000000 INFO @ Sat, 24 Aug 2019 21:05:24: 17000000 INFO @ Sat, 24 Aug 2019 21:05:31: 11000000 INFO @ Sat, 24 Aug 2019 21:05:35: 18000000 INFO @ Sat, 24 Aug 2019 21:05:36: 11000000 INFO @ Sat, 24 Aug 2019 21:05:45: 19000000 INFO @ Sat, 24 Aug 2019 21:05:47: 12000000 INFO @ Sat, 24 Aug 2019 21:05:48: 12000000 INFO @ Sat, 24 Aug 2019 21:05:56: 20000000 INFO @ Sat, 24 Aug 2019 21:06:00: 13000000 INFO @ Sat, 24 Aug 2019 21:06:03: 13000000 INFO @ Sat, 24 Aug 2019 21:06:07: 21000000 INFO @ Sat, 24 Aug 2019 21:06:12: 14000000 INFO @ Sat, 24 Aug 2019 21:06:18: 22000000 INFO @ Sat, 24 Aug 2019 21:06:19: 14000000 INFO @ Sat, 24 Aug 2019 21:06:25: 15000000 INFO @ Sat, 24 Aug 2019 21:06:29: 23000000 INFO @ Sat, 24 Aug 2019 21:06:34: 15000000 INFO @ Sat, 24 Aug 2019 21:06:37: 16000000 INFO @ Sat, 24 Aug 2019 21:06:40: 24000000 INFO @ Sat, 24 Aug 2019 21:06:51: 16000000 INFO @ Sat, 24 Aug 2019 21:06:51: 25000000 INFO @ Sat, 24 Aug 2019 21:06:52: 17000000 INFO @ Sat, 24 Aug 2019 21:07:03: 26000000 INFO @ Sat, 24 Aug 2019 21:07:05: 18000000 INFO @ Sat, 24 Aug 2019 21:07:07: 17000000 INFO @ Sat, 24 Aug 2019 21:07:14: 27000000 INFO @ Sat, 24 Aug 2019 21:07:18: 19000000 INFO @ Sat, 24 Aug 2019 21:07:24: 18000000 INFO @ Sat, 24 Aug 2019 21:07:25: 28000000 INFO @ Sat, 24 Aug 2019 21:07:33: 20000000 INFO @ Sat, 24 Aug 2019 21:07:36: 29000000 INFO @ Sat, 24 Aug 2019 21:07:40: 19000000 INFO @ Sat, 24 Aug 2019 21:07:47: 30000000 INFO @ Sat, 24 Aug 2019 21:07:48: 21000000 INFO @ Sat, 24 Aug 2019 21:07:56: 20000000 INFO @ Sat, 24 Aug 2019 21:07:59: 31000000 INFO @ Sat, 24 Aug 2019 21:08:03: 22000000 INFO @ Sat, 24 Aug 2019 21:08:11: 32000000 INFO @ Sat, 24 Aug 2019 21:08:13: 21000000 INFO @ Sat, 24 Aug 2019 21:08:18: 23000000 INFO @ Sat, 24 Aug 2019 21:08:23: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:08:23: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:08:23: #1 total tags in treatment: 32995399 INFO @ Sat, 24 Aug 2019 21:08:23: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:08:23: #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 21:08:24: #1 tags after filtering in treatment: 32995301 INFO @ Sat, 24 Aug 2019 21:08:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:08:24: #1 finished! INFO @ Sat, 24 Aug 2019 21:08:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:08:28: #2 number of paired peaks: 6235 INFO @ Sat, 24 Aug 2019 21:08:28: start model_add_line... INFO @ Sat, 24 Aug 2019 21:08:28: start X-correlation... INFO @ Sat, 24 Aug 2019 21:08:28: end of X-cor INFO @ Sat, 24 Aug 2019 21:08:28: #2 finished! INFO @ Sat, 24 Aug 2019 21:08:28: #2 predicted fragment length is 101 bps INFO @ Sat, 24 Aug 2019 21:08:28: #2 alternative fragment length(s) may be 101,568 bps INFO @ Sat, 24 Aug 2019 21:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.05_model.r WARNING @ Sat, 24 Aug 2019 21:08:28: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:08:28: #2 You may need to consider one of the other alternative d(s): 101,568 WARNING @ Sat, 24 Aug 2019 21:08:28: #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 21:08:28: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:08:29: 22000000 INFO @ Sat, 24 Aug 2019 21:08:32: 24000000 INFO @ Sat, 24 Aug 2019 21:08:44: 23000000 INFO @ Sat, 24 Aug 2019 21:08:47: 25000000 INFO @ Sat, 24 Aug 2019 21:08:59: 24000000 INFO @ Sat, 24 Aug 2019 21:09:02: 26000000 INFO @ Sat, 24 Aug 2019 21:09:13: 25000000 INFO @ Sat, 24 Aug 2019 21:09:17: 27000000 INFO @ Sat, 24 Aug 2019 21:09:28: 26000000 INFO @ Sat, 24 Aug 2019 21:09:32: 28000000 INFO @ Sat, 24 Aug 2019 21:09:43: 27000000 INFO @ Sat, 24 Aug 2019 21:09:47: 29000000 INFO @ Sat, 24 Aug 2019 21:09:59: 28000000 INFO @ Sat, 24 Aug 2019 21:10:04: 30000000 INFO @ Sat, 24 Aug 2019 21:10:15: 29000000 INFO @ Sat, 24 Aug 2019 21:10:20: 31000000 INFO @ Sat, 24 Aug 2019 21:10:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:10:30: 30000000 INFO @ Sat, 24 Aug 2019 21:10:36: 32000000 INFO @ Sat, 24 Aug 2019 21:10:45: 31000000 INFO @ Sat, 24 Aug 2019 21:10:51: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:10:51: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:10:51: #1 total tags in treatment: 32995399 INFO @ Sat, 24 Aug 2019 21:10:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:10:51: #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 21:10:52: #1 tags after filtering in treatment: 32995301 INFO @ Sat, 24 Aug 2019 21:10:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:10:52: #1 finished! INFO @ Sat, 24 Aug 2019 21:10:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:10:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:10:56: #2 number of paired peaks: 6235 INFO @ Sat, 24 Aug 2019 21:10:56: start model_add_line... INFO @ Sat, 24 Aug 2019 21:10:56: start X-correlation... INFO @ Sat, 24 Aug 2019 21:10:56: end of X-cor INFO @ Sat, 24 Aug 2019 21:10:56: #2 finished! INFO @ Sat, 24 Aug 2019 21:10:56: #2 predicted fragment length is 101 bps INFO @ Sat, 24 Aug 2019 21:10:56: #2 alternative fragment length(s) may be 101,568 bps INFO @ Sat, 24 Aug 2019 21:10:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.20_model.r WARNING @ Sat, 24 Aug 2019 21:10:56: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:10:56: #2 You may need to consider one of the other alternative d(s): 101,568 WARNING @ Sat, 24 Aug 2019 21:10:56: #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 21:10:56: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:10:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:10:59: 32000000 INFO @ Sat, 24 Aug 2019 21:11:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.05_peaks.xls INFO @ Sat, 24 Aug 2019 21:11:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:11:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.05_summits.bed INFO @ Sat, 24 Aug 2019 21:11:12: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (2572 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:11:13: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:11:13: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:11:13: #1 total tags in treatment: 32995399 INFO @ Sat, 24 Aug 2019 21:11:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:11:13: #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 21:11:14: #1 tags after filtering in treatment: 32995301 INFO @ Sat, 24 Aug 2019 21:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:11:14: #1 finished! INFO @ Sat, 24 Aug 2019 21:11:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:11:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:11:18: #2 number of paired peaks: 6235 INFO @ Sat, 24 Aug 2019 21:11:18: start model_add_line... INFO @ Sat, 24 Aug 2019 21:11:18: start X-correlation... INFO @ Sat, 24 Aug 2019 21:11:18: end of X-cor INFO @ Sat, 24 Aug 2019 21:11:18: #2 finished! INFO @ Sat, 24 Aug 2019 21:11:18: #2 predicted fragment length is 101 bps INFO @ Sat, 24 Aug 2019 21:11:18: #2 alternative fragment length(s) may be 101,568 bps INFO @ Sat, 24 Aug 2019 21:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.10_model.r WARNING @ Sat, 24 Aug 2019 21:11:18: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:11:18: #2 You may need to consider one of the other alternative d(s): 101,568 WARNING @ Sat, 24 Aug 2019 21:11:18: #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 21:11:18: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:12:40: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:13:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.20_peaks.xls INFO @ Sat, 24 Aug 2019 21:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.20_summits.bed INFO @ Sat, 24 Aug 2019 21:13:31: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:13:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.10_peaks.xls INFO @ Sat, 24 Aug 2019 21:13:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:13:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX754756/SRX754756.10_summits.bed INFO @ Sat, 24 Aug 2019 21:13:52: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1144 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。