Job ID = 2640445 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:53:02 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 ) 2019-08-24T07:53:02 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:57:06 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 ) 2019-08-24T07:58:23 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 ) 2019-08-24T07:59:18 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 ) 2019-08-24T07:59:18 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 ) 2019-08-24T08:00:43 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 ) 2019-08-24T08:00:49 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 ) 2019-08-24T08:00:57 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 : 34,718,157 reads read : 69,436,314 reads written : 34,718,157 reads 0-length : 34,718,157 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:29 34718157 reads; of these: 34718157 (100.00%) were unpaired; of these: 3773032 (10.87%) aligned 0 times 23690673 (68.24%) aligned exactly 1 time 7254452 (20.90%) aligned >1 times 89.13% overall alignment rate Time searching: 00:29:32 Overall time: 00:29:32 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] 1360771 / 30945125 = 0.0440 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.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 17:59:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:59:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:59:47: 1000000 INFO @ Sat, 24 Aug 2019 17:59:56: 2000000 INFO @ Sat, 24 Aug 2019 18:00:05: 3000000 INFO @ Sat, 24 Aug 2019 18:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.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 18:00:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:00:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:00:14: 4000000 INFO @ Sat, 24 Aug 2019 18:00:21: 1000000 INFO @ Sat, 24 Aug 2019 18:00:23: 5000000 INFO @ Sat, 24 Aug 2019 18:00:32: 6000000 INFO @ Sat, 24 Aug 2019 18:00:34: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.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 18:00:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:00:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:00:41: 7000000 INFO @ Sat, 24 Aug 2019 18:00:47: 3000000 INFO @ Sat, 24 Aug 2019 18:00:47: 1000000 INFO @ Sat, 24 Aug 2019 18:00:50: 8000000 INFO @ Sat, 24 Aug 2019 18:00:56: 2000000 INFO @ Sat, 24 Aug 2019 18:01:00: 4000000 INFO @ Sat, 24 Aug 2019 18:01:00: 9000000 INFO @ Sat, 24 Aug 2019 18:01:06: 3000000 INFO @ Sat, 24 Aug 2019 18:01:09: 10000000 INFO @ Sat, 24 Aug 2019 18:01:12: 5000000 INFO @ Sat, 24 Aug 2019 18:01:15: 4000000 INFO @ Sat, 24 Aug 2019 18:01:18: 11000000 INFO @ Sat, 24 Aug 2019 18:01:25: 5000000 INFO @ Sat, 24 Aug 2019 18:01:25: 6000000 INFO @ Sat, 24 Aug 2019 18:01:28: 12000000 INFO @ Sat, 24 Aug 2019 18:01:34: 6000000 INFO @ Sat, 24 Aug 2019 18:01:37: 13000000 INFO @ Sat, 24 Aug 2019 18:01:38: 7000000 INFO @ Sat, 24 Aug 2019 18:01:43: 7000000 INFO @ Sat, 24 Aug 2019 18:01:47: 14000000 INFO @ Sat, 24 Aug 2019 18:01:51: 8000000 INFO @ Sat, 24 Aug 2019 18:01:53: 8000000 INFO @ Sat, 24 Aug 2019 18:01:56: 15000000 INFO @ Sat, 24 Aug 2019 18:02:02: 9000000 INFO @ Sat, 24 Aug 2019 18:02:04: 9000000 INFO @ Sat, 24 Aug 2019 18:02:05: 16000000 INFO @ Sat, 24 Aug 2019 18:02:12: 10000000 INFO @ Sat, 24 Aug 2019 18:02:15: 17000000 INFO @ Sat, 24 Aug 2019 18:02:16: 10000000 INFO @ Sat, 24 Aug 2019 18:02:21: 11000000 INFO @ Sat, 24 Aug 2019 18:02:24: 18000000 INFO @ Sat, 24 Aug 2019 18:02:27: 11000000 INFO @ Sat, 24 Aug 2019 18:02:31: 12000000 INFO @ Sat, 24 Aug 2019 18:02:33: 19000000 INFO @ Sat, 24 Aug 2019 18:02:39: 12000000 INFO @ Sat, 24 Aug 2019 18:02:40: 13000000 INFO @ Sat, 24 Aug 2019 18:02:42: 20000000 INFO @ Sat, 24 Aug 2019 18:02:49: 14000000 INFO @ Sat, 24 Aug 2019 18:02:52: 21000000 INFO @ Sat, 24 Aug 2019 18:02:52: 13000000 INFO @ Sat, 24 Aug 2019 18:02:59: 15000000 INFO @ Sat, 24 Aug 2019 18:03:01: 22000000 INFO @ Sat, 24 Aug 2019 18:03:04: 14000000 INFO @ Sat, 24 Aug 2019 18:03:08: 16000000 INFO @ Sat, 24 Aug 2019 18:03:10: 23000000 INFO @ Sat, 24 Aug 2019 18:03:16: 15000000 INFO @ Sat, 24 Aug 2019 18:03:18: 17000000 INFO @ Sat, 24 Aug 2019 18:03:20: 24000000 INFO @ Sat, 24 Aug 2019 18:03:27: 18000000 INFO @ Sat, 24 Aug 2019 18:03:27: 16000000 INFO @ Sat, 24 Aug 2019 18:03:28: 25000000 INFO @ Sat, 24 Aug 2019 18:03:36: 19000000 INFO @ Sat, 24 Aug 2019 18:03:37: 26000000 INFO @ Sat, 24 Aug 2019 18:03:39: 17000000 INFO @ Sat, 24 Aug 2019 18:03:45: 20000000 INFO @ Sat, 24 Aug 2019 18:03:46: 27000000 INFO @ Sat, 24 Aug 2019 18:03:52: 18000000 INFO @ Sat, 24 Aug 2019 18:03:54: 21000000 INFO @ Sat, 24 Aug 2019 18:03:54: 28000000 INFO @ Sat, 24 Aug 2019 18:04:04: 22000000 INFO @ Sat, 24 Aug 2019 18:04:04: 29000000 INFO @ Sat, 24 Aug 2019 18:04:04: 19000000 INFO @ Sat, 24 Aug 2019 18:04:10: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 18:04:10: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 18:04:10: #1 total tags in treatment: 29584354 INFO @ Sat, 24 Aug 2019 18:04:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:04:10: #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 18:04:10: #1 tags after filtering in treatment: 29584259 INFO @ Sat, 24 Aug 2019 18:04:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:04:10: #1 finished! INFO @ Sat, 24 Aug 2019 18:04:10: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:04:13: 23000000 INFO @ Sat, 24 Aug 2019 18:04:14: #2 number of paired peaks: 5182 INFO @ Sat, 24 Aug 2019 18:04:14: start model_add_line... INFO @ Sat, 24 Aug 2019 18:04:14: start X-correlation... INFO @ Sat, 24 Aug 2019 18:04:14: end of X-cor INFO @ Sat, 24 Aug 2019 18:04:14: #2 finished! INFO @ Sat, 24 Aug 2019 18:04:14: #2 predicted fragment length is 77 bps INFO @ Sat, 24 Aug 2019 18:04:14: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 24 Aug 2019 18:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.05_model.r WARNING @ Sat, 24 Aug 2019 18:04:14: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:04:14: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 24 Aug 2019 18:04:14: #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 18:04:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:04:17: 20000000 INFO @ Sat, 24 Aug 2019 18:04:22: 24000000 INFO @ Sat, 24 Aug 2019 18:04:29: 21000000 INFO @ Sat, 24 Aug 2019 18:04:31: 25000000 INFO @ Sat, 24 Aug 2019 18:04:40: 26000000 INFO @ Sat, 24 Aug 2019 18:04:41: 22000000 INFO @ Sat, 24 Aug 2019 18:04:49: 27000000 INFO @ Sat, 24 Aug 2019 18:04:54: 23000000 INFO @ Sat, 24 Aug 2019 18:04:58: 28000000 INFO @ Sat, 24 Aug 2019 18:05:05: 24000000 INFO @ Sat, 24 Aug 2019 18:05:07: 29000000 INFO @ Sat, 24 Aug 2019 18:05:13: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 18:05:13: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 18:05:13: #1 total tags in treatment: 29584354 INFO @ Sat, 24 Aug 2019 18:05:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:05:13: #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 18:05:13: #1 tags after filtering in treatment: 29584259 INFO @ Sat, 24 Aug 2019 18:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:05:13: #1 finished! INFO @ Sat, 24 Aug 2019 18:05:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:05:17: #2 number of paired peaks: 5182 INFO @ Sat, 24 Aug 2019 18:05:17: start model_add_line... INFO @ Sat, 24 Aug 2019 18:05:17: start X-correlation... INFO @ Sat, 24 Aug 2019 18:05:17: end of X-cor INFO @ Sat, 24 Aug 2019 18:05:17: #2 finished! INFO @ Sat, 24 Aug 2019 18:05:17: #2 predicted fragment length is 77 bps INFO @ Sat, 24 Aug 2019 18:05:17: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 24 Aug 2019 18:05:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.20_model.r WARNING @ Sat, 24 Aug 2019 18:05:17: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:05:17: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 24 Aug 2019 18:05:17: #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 18:05:17: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:05:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:05:17: 25000000 INFO @ Sat, 24 Aug 2019 18:05:30: 26000000 INFO @ Sat, 24 Aug 2019 18:05:42: 27000000 INFO @ Sat, 24 Aug 2019 18:05:47: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:05:54: 28000000 INFO @ Sat, 24 Aug 2019 18:06:06: 29000000 INFO @ Sat, 24 Aug 2019 18:06:13: #1 tag size is determined as 75 bps INFO @ Sat, 24 Aug 2019 18:06:13: #1 tag size = 75 INFO @ Sat, 24 Aug 2019 18:06:13: #1 total tags in treatment: 29584354 INFO @ Sat, 24 Aug 2019 18:06:13: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:06:13: #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 18:06:14: #1 tags after filtering in treatment: 29584259 INFO @ Sat, 24 Aug 2019 18:06:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:06:14: #1 finished! INFO @ Sat, 24 Aug 2019 18:06:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:06:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:06:17: #2 number of paired peaks: 5182 INFO @ Sat, 24 Aug 2019 18:06:17: start model_add_line... INFO @ Sat, 24 Aug 2019 18:06:17: start X-correlation... INFO @ Sat, 24 Aug 2019 18:06:17: end of X-cor INFO @ Sat, 24 Aug 2019 18:06:17: #2 finished! INFO @ Sat, 24 Aug 2019 18:06:17: #2 predicted fragment length is 77 bps INFO @ Sat, 24 Aug 2019 18:06:17: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 24 Aug 2019 18:06:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.10_model.r WARNING @ Sat, 24 Aug 2019 18:06:17: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 18:06:17: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 24 Aug 2019 18:06:17: #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 18:06:17: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:06:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.05_summits.bed INFO @ Sat, 24 Aug 2019 18:06:35: Done! pass1 - making usageList (84 chroms): 2 millis pass2 - checking and writing primary data (5352 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:06:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:07:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:07:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:07:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.20_summits.bed INFO @ Sat, 24 Aug 2019 18:07:38: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:07:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:08:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:08:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:08:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4320111/SRX4320111.10_summits.bed INFO @ Sat, 24 Aug 2019 18:08:41: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (1932 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。