Job ID = 2001561 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:04:34 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 ) 2019-07-04T20:06:03 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 ) 2019-07-04T20:06:35 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 : 56,779,036 reads read : 56,779,036 reads written : 56,779,036 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:23:20 56779036 reads; of these: 56779036 (100.00%) were unpaired; of these: 1353033 (2.38%) aligned 0 times 40643960 (71.58%) aligned exactly 1 time 14782043 (26.03%) aligned >1 times 97.62% overall alignment rate Time searching: 01:23:21 Overall time: 01:23:21 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 24 files... [bam_rmdupse_core] 4112409 / 55426003 = 0.0742 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 06:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.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 @ Fri, 05 Jul 2019 06:57:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:57:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.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 @ Fri, 05 Jul 2019 06:57:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:57:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:57:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.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 @ Fri, 05 Jul 2019 06:57:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:57:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:57:41: 1000000 INFO @ Fri, 05 Jul 2019 06:57:41: 1000000 INFO @ Fri, 05 Jul 2019 06:57:43: 1000000 INFO @ Fri, 05 Jul 2019 06:57:49: 2000000 INFO @ Fri, 05 Jul 2019 06:57:50: 2000000 INFO @ Fri, 05 Jul 2019 06:57:52: 2000000 INFO @ Fri, 05 Jul 2019 06:57:57: 3000000 INFO @ Fri, 05 Jul 2019 06:58:00: 3000000 INFO @ Fri, 05 Jul 2019 06:58:02: 3000000 INFO @ Fri, 05 Jul 2019 06:58:05: 4000000 INFO @ Fri, 05 Jul 2019 06:58:09: 4000000 INFO @ Fri, 05 Jul 2019 06:58:11: 4000000 INFO @ Fri, 05 Jul 2019 06:58:14: 5000000 INFO @ Fri, 05 Jul 2019 06:58:18: 5000000 INFO @ Fri, 05 Jul 2019 06:58:20: 5000000 INFO @ Fri, 05 Jul 2019 06:58:22: 6000000 INFO @ Fri, 05 Jul 2019 06:58:28: 6000000 INFO @ Fri, 05 Jul 2019 06:58:29: 6000000 INFO @ Fri, 05 Jul 2019 06:58:30: 7000000 INFO @ Fri, 05 Jul 2019 06:58:37: 7000000 INFO @ Fri, 05 Jul 2019 06:58:38: 8000000 INFO @ Fri, 05 Jul 2019 06:58:38: 7000000 INFO @ Fri, 05 Jul 2019 06:58:46: 9000000 INFO @ Fri, 05 Jul 2019 06:58:46: 8000000 INFO @ Fri, 05 Jul 2019 06:58:47: 8000000 INFO @ Fri, 05 Jul 2019 06:58:54: 10000000 INFO @ Fri, 05 Jul 2019 06:58:56: 9000000 INFO @ Fri, 05 Jul 2019 06:58:56: 9000000 INFO @ Fri, 05 Jul 2019 06:59:02: 11000000 INFO @ Fri, 05 Jul 2019 06:59:05: 10000000 INFO @ Fri, 05 Jul 2019 06:59:06: 10000000 INFO @ Fri, 05 Jul 2019 06:59:10: 12000000 INFO @ Fri, 05 Jul 2019 06:59:15: 11000000 INFO @ Fri, 05 Jul 2019 06:59:15: 11000000 INFO @ Fri, 05 Jul 2019 06:59:19: 13000000 INFO @ Fri, 05 Jul 2019 06:59:24: 12000000 INFO @ Fri, 05 Jul 2019 06:59:24: 12000000 INFO @ Fri, 05 Jul 2019 06:59:27: 14000000 INFO @ Fri, 05 Jul 2019 06:59:33: 13000000 INFO @ Fri, 05 Jul 2019 06:59:34: 13000000 INFO @ Fri, 05 Jul 2019 06:59:35: 15000000 INFO @ Fri, 05 Jul 2019 06:59:43: 16000000 INFO @ Fri, 05 Jul 2019 06:59:43: 14000000 INFO @ Fri, 05 Jul 2019 06:59:43: 14000000 INFO @ Fri, 05 Jul 2019 06:59:51: 17000000 INFO @ Fri, 05 Jul 2019 06:59:52: 15000000 INFO @ Fri, 05 Jul 2019 06:59:52: 15000000 INFO @ Fri, 05 Jul 2019 06:59:59: 18000000 INFO @ Fri, 05 Jul 2019 07:00:02: 16000000 INFO @ Fri, 05 Jul 2019 07:00:02: 16000000 INFO @ Fri, 05 Jul 2019 07:00:07: 19000000 INFO @ Fri, 05 Jul 2019 07:00:11: 17000000 INFO @ Fri, 05 Jul 2019 07:00:11: 17000000 INFO @ Fri, 05 Jul 2019 07:00:15: 20000000 INFO @ Fri, 05 Jul 2019 07:00:20: 18000000 INFO @ Fri, 05 Jul 2019 07:00:20: 18000000 INFO @ Fri, 05 Jul 2019 07:00:23: 21000000 INFO @ Fri, 05 Jul 2019 07:00:30: 19000000 INFO @ Fri, 05 Jul 2019 07:00:30: 19000000 INFO @ Fri, 05 Jul 2019 07:00:31: 22000000 INFO @ Fri, 05 Jul 2019 07:00:39: 23000000 INFO @ Fri, 05 Jul 2019 07:00:39: 20000000 INFO @ Fri, 05 Jul 2019 07:00:39: 20000000 INFO @ Fri, 05 Jul 2019 07:00:47: 24000000 INFO @ Fri, 05 Jul 2019 07:00:48: 21000000 INFO @ Fri, 05 Jul 2019 07:00:48: 21000000 INFO @ Fri, 05 Jul 2019 07:00:55: 25000000 INFO @ Fri, 05 Jul 2019 07:00:58: 22000000 INFO @ Fri, 05 Jul 2019 07:00:58: 22000000 INFO @ Fri, 05 Jul 2019 07:01:03: 26000000 INFO @ Fri, 05 Jul 2019 07:01:07: 23000000 INFO @ Fri, 05 Jul 2019 07:01:07: 23000000 INFO @ Fri, 05 Jul 2019 07:01:11: 27000000 INFO @ Fri, 05 Jul 2019 07:01:16: 24000000 INFO @ Fri, 05 Jul 2019 07:01:17: 24000000 INFO @ Fri, 05 Jul 2019 07:01:19: 28000000 INFO @ Fri, 05 Jul 2019 07:01:25: 25000000 INFO @ Fri, 05 Jul 2019 07:01:26: 25000000 INFO @ Fri, 05 Jul 2019 07:01:27: 29000000 INFO @ Fri, 05 Jul 2019 07:01:34: 26000000 INFO @ Fri, 05 Jul 2019 07:01:35: 30000000 INFO @ Fri, 05 Jul 2019 07:01:35: 26000000 INFO @ Fri, 05 Jul 2019 07:01:43: 31000000 INFO @ Fri, 05 Jul 2019 07:01:43: 27000000 INFO @ Fri, 05 Jul 2019 07:01:44: 27000000 INFO @ Fri, 05 Jul 2019 07:01:51: 32000000 INFO @ Fri, 05 Jul 2019 07:01:53: 28000000 INFO @ Fri, 05 Jul 2019 07:01:54: 28000000 INFO @ Fri, 05 Jul 2019 07:01:59: 33000000 INFO @ Fri, 05 Jul 2019 07:02:02: 29000000 INFO @ Fri, 05 Jul 2019 07:02:03: 29000000 INFO @ Fri, 05 Jul 2019 07:02:07: 34000000 INFO @ Fri, 05 Jul 2019 07:02:11: 30000000 INFO @ Fri, 05 Jul 2019 07:02:12: 30000000 INFO @ Fri, 05 Jul 2019 07:02:15: 35000000 INFO @ Fri, 05 Jul 2019 07:02:20: 31000000 INFO @ Fri, 05 Jul 2019 07:02:21: 31000000 INFO @ Fri, 05 Jul 2019 07:02:23: 36000000 INFO @ Fri, 05 Jul 2019 07:02:29: 32000000 INFO @ Fri, 05 Jul 2019 07:02:30: 32000000 INFO @ Fri, 05 Jul 2019 07:02:31: 37000000 INFO @ Fri, 05 Jul 2019 07:02:38: 33000000 INFO @ Fri, 05 Jul 2019 07:02:38: 38000000 INFO @ Fri, 05 Jul 2019 07:02:38: 33000000 INFO @ Fri, 05 Jul 2019 07:02:46: 39000000 INFO @ Fri, 05 Jul 2019 07:02:47: 34000000 INFO @ Fri, 05 Jul 2019 07:02:48: 34000000 INFO @ Fri, 05 Jul 2019 07:02:54: 40000000 INFO @ Fri, 05 Jul 2019 07:02:56: 35000000 INFO @ Fri, 05 Jul 2019 07:02:57: 35000000 INFO @ Fri, 05 Jul 2019 07:03:02: 41000000 INFO @ Fri, 05 Jul 2019 07:03:05: 36000000 INFO @ Fri, 05 Jul 2019 07:03:06: 36000000 INFO @ Fri, 05 Jul 2019 07:03:10: 42000000 INFO @ Fri, 05 Jul 2019 07:03:14: 37000000 INFO @ Fri, 05 Jul 2019 07:03:15: 37000000 INFO @ Fri, 05 Jul 2019 07:03:18: 43000000 INFO @ Fri, 05 Jul 2019 07:03:23: 38000000 INFO @ Fri, 05 Jul 2019 07:03:24: 38000000 INFO @ Fri, 05 Jul 2019 07:03:27: 44000000 INFO @ Fri, 05 Jul 2019 07:03:32: 39000000 INFO @ Fri, 05 Jul 2019 07:03:32: 39000000 INFO @ Fri, 05 Jul 2019 07:03:36: 45000000 INFO @ Fri, 05 Jul 2019 07:03:41: 40000000 INFO @ Fri, 05 Jul 2019 07:03:41: 40000000 INFO @ Fri, 05 Jul 2019 07:03:44: 46000000 INFO @ Fri, 05 Jul 2019 07:03:50: 41000000 INFO @ Fri, 05 Jul 2019 07:03:50: 41000000 INFO @ Fri, 05 Jul 2019 07:03:53: 47000000 INFO @ Fri, 05 Jul 2019 07:03:59: 42000000 INFO @ Fri, 05 Jul 2019 07:03:59: 42000000 INFO @ Fri, 05 Jul 2019 07:04:02: 48000000 INFO @ Fri, 05 Jul 2019 07:04:08: 43000000 INFO @ Fri, 05 Jul 2019 07:04:08: 43000000 INFO @ Fri, 05 Jul 2019 07:04:10: 49000000 INFO @ Fri, 05 Jul 2019 07:04:18: 44000000 INFO @ Fri, 05 Jul 2019 07:04:18: 44000000 INFO @ Fri, 05 Jul 2019 07:04:19: 50000000 INFO @ Fri, 05 Jul 2019 07:04:27: 51000000 INFO @ Fri, 05 Jul 2019 07:04:28: 45000000 INFO @ Fri, 05 Jul 2019 07:04:28: 45000000 INFO @ Fri, 05 Jul 2019 07:04:31: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:04:31: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:04:31: #1 total tags in treatment: 51313594 INFO @ Fri, 05 Jul 2019 07:04:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:04:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 07:04:32: #1 tags after filtering in treatment: 51313500 INFO @ Fri, 05 Jul 2019 07:04:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:04:32: #1 finished! INFO @ Fri, 05 Jul 2019 07:04:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:04:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:04:38: 46000000 INFO @ Fri, 05 Jul 2019 07:04:38: 46000000 INFO @ Fri, 05 Jul 2019 07:04:38: #2 number of paired peaks: 20725 INFO @ Fri, 05 Jul 2019 07:04:38: start model_add_line... INFO @ Fri, 05 Jul 2019 07:04:39: start X-correlation... INFO @ Fri, 05 Jul 2019 07:04:39: end of X-cor INFO @ Fri, 05 Jul 2019 07:04:39: #2 finished! INFO @ Fri, 05 Jul 2019 07:04:39: #2 predicted fragment length is 110 bps INFO @ Fri, 05 Jul 2019 07:04:39: #2 alternative fragment length(s) may be 4,110,275,492 bps INFO @ Fri, 05 Jul 2019 07:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.10_model.r INFO @ Fri, 05 Jul 2019 07:04:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:04:48: 47000000 INFO @ Fri, 05 Jul 2019 07:04:48: 47000000 INFO @ Fri, 05 Jul 2019 07:04:58: 48000000 INFO @ Fri, 05 Jul 2019 07:04:58: 48000000 INFO @ Fri, 05 Jul 2019 07:05:08: 49000000 INFO @ Fri, 05 Jul 2019 07:05:08: 49000000 INFO @ Fri, 05 Jul 2019 07:05:18: 50000000 INFO @ Fri, 05 Jul 2019 07:05:18: 50000000 INFO @ Fri, 05 Jul 2019 07:05:27: 51000000 INFO @ Fri, 05 Jul 2019 07:05:27: 51000000 INFO @ Fri, 05 Jul 2019 07:05:31: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:05:31: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:05:31: #1 total tags in treatment: 51313594 INFO @ Fri, 05 Jul 2019 07:05:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:05:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 07:05:31: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:05:31: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:05:31: #1 total tags in treatment: 51313594 INFO @ Fri, 05 Jul 2019 07:05:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:05:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 07:05:32: #1 tags after filtering in treatment: 51313500 INFO @ Fri, 05 Jul 2019 07:05:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:05:32: #1 finished! INFO @ Fri, 05 Jul 2019 07:05:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:05:32: #1 tags after filtering in treatment: 51313500 INFO @ Fri, 05 Jul 2019 07:05:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:05:32: #1 finished! INFO @ Fri, 05 Jul 2019 07:05:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:05:39: #2 number of paired peaks: 20725 INFO @ Fri, 05 Jul 2019 07:05:39: start model_add_line... INFO @ Fri, 05 Jul 2019 07:05:39: #2 number of paired peaks: 20725 INFO @ Fri, 05 Jul 2019 07:05:39: start model_add_line... INFO @ Fri, 05 Jul 2019 07:05:39: start X-correlation... INFO @ Fri, 05 Jul 2019 07:05:39: end of X-cor INFO @ Fri, 05 Jul 2019 07:05:39: #2 finished! INFO @ Fri, 05 Jul 2019 07:05:39: #2 predicted fragment length is 110 bps INFO @ Fri, 05 Jul 2019 07:05:39: #2 alternative fragment length(s) may be 4,110,275,492 bps INFO @ Fri, 05 Jul 2019 07:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.20_model.r INFO @ Fri, 05 Jul 2019 07:05:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:05:39: start X-correlation... INFO @ Fri, 05 Jul 2019 07:05:39: end of X-cor INFO @ Fri, 05 Jul 2019 07:05:39: #2 finished! INFO @ Fri, 05 Jul 2019 07:05:39: #2 predicted fragment length is 110 bps INFO @ Fri, 05 Jul 2019 07:05:39: #2 alternative fragment length(s) may be 4,110,275,492 bps INFO @ Fri, 05 Jul 2019 07:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.05_model.r INFO @ Fri, 05 Jul 2019 07:05:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:05:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:07:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:08:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:08:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.10_summits.bed INFO @ Fri, 05 Jul 2019 07:09:05: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (1913 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.20_summits.bed INFO @ Fri, 05 Jul 2019 07:09:59: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (380 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101904/ERX101904.05_summits.bed INFO @ Fri, 05 Jul 2019 07:10:08: Done! pass1 - making usageList (91 chroms): 5 millis pass2 - checking and writing primary data (7366 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。