Job ID = 2001697 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T00:03:40 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 ) spots read : 73,015,637 reads read : 73,015,637 reads written : 73,015,637 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: 00:00:02 Multiseed full-index search: 01:20:28 73015637 reads; of these: 73015637 (100.00%) were unpaired; of these: 1598310 (2.19%) aligned 0 times 59453604 (81.43%) aligned exactly 1 time 11963723 (16.39%) aligned >1 times 97.81% overall alignment rate Time searching: 01:20:32 Overall time: 01:20:32 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 32 files... [bam_rmdupse_core] 17855271 / 71417327 = 0.2500 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 10:58:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.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 10:58:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:58:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:58:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.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 10:58:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:58:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.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 10:58:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:58:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:59:00: 1000000 INFO @ Fri, 05 Jul 2019 10:59:01: 1000000 INFO @ Fri, 05 Jul 2019 10:59:03: 1000000 INFO @ Fri, 05 Jul 2019 10:59:08: 2000000 INFO @ Fri, 05 Jul 2019 10:59:10: 2000000 INFO @ Fri, 05 Jul 2019 10:59:13: 2000000 INFO @ Fri, 05 Jul 2019 10:59:16: 3000000 INFO @ Fri, 05 Jul 2019 10:59:18: 3000000 INFO @ Fri, 05 Jul 2019 10:59:23: 3000000 INFO @ Fri, 05 Jul 2019 10:59:24: 4000000 INFO @ Fri, 05 Jul 2019 10:59:27: 4000000 INFO @ Fri, 05 Jul 2019 10:59:31: 5000000 INFO @ Fri, 05 Jul 2019 10:59:33: 4000000 INFO @ Fri, 05 Jul 2019 10:59:36: 5000000 INFO @ Fri, 05 Jul 2019 10:59:39: 6000000 INFO @ Fri, 05 Jul 2019 10:59:43: 5000000 INFO @ Fri, 05 Jul 2019 10:59:44: 6000000 INFO @ Fri, 05 Jul 2019 10:59:47: 7000000 INFO @ Fri, 05 Jul 2019 10:59:53: 6000000 INFO @ Fri, 05 Jul 2019 10:59:53: 7000000 INFO @ Fri, 05 Jul 2019 10:59:55: 8000000 INFO @ Fri, 05 Jul 2019 11:00:01: 8000000 INFO @ Fri, 05 Jul 2019 11:00:02: 7000000 INFO @ Fri, 05 Jul 2019 11:00:03: 9000000 INFO @ Fri, 05 Jul 2019 11:00:10: 9000000 INFO @ Fri, 05 Jul 2019 11:00:11: 10000000 INFO @ Fri, 05 Jul 2019 11:00:12: 8000000 INFO @ Fri, 05 Jul 2019 11:00:19: 10000000 INFO @ Fri, 05 Jul 2019 11:00:19: 11000000 INFO @ Fri, 05 Jul 2019 11:00:22: 9000000 INFO @ Fri, 05 Jul 2019 11:00:27: 12000000 INFO @ Fri, 05 Jul 2019 11:00:27: 11000000 INFO @ Fri, 05 Jul 2019 11:00:32: 10000000 INFO @ Fri, 05 Jul 2019 11:00:35: 13000000 INFO @ Fri, 05 Jul 2019 11:00:36: 12000000 INFO @ Fri, 05 Jul 2019 11:00:42: 11000000 INFO @ Fri, 05 Jul 2019 11:00:43: 14000000 INFO @ Fri, 05 Jul 2019 11:00:44: 13000000 INFO @ Fri, 05 Jul 2019 11:00:51: 15000000 INFO @ Fri, 05 Jul 2019 11:00:51: 12000000 INFO @ Fri, 05 Jul 2019 11:00:53: 14000000 INFO @ Fri, 05 Jul 2019 11:00:59: 16000000 INFO @ Fri, 05 Jul 2019 11:01:01: 15000000 INFO @ Fri, 05 Jul 2019 11:01:01: 13000000 INFO @ Fri, 05 Jul 2019 11:01:06: 17000000 INFO @ Fri, 05 Jul 2019 11:01:09: 16000000 INFO @ Fri, 05 Jul 2019 11:01:11: 14000000 INFO @ Fri, 05 Jul 2019 11:01:14: 18000000 INFO @ Fri, 05 Jul 2019 11:01:18: 17000000 INFO @ Fri, 05 Jul 2019 11:01:20: 15000000 INFO @ Fri, 05 Jul 2019 11:01:22: 19000000 INFO @ Fri, 05 Jul 2019 11:01:26: 18000000 INFO @ Fri, 05 Jul 2019 11:01:30: 20000000 INFO @ Fri, 05 Jul 2019 11:01:30: 16000000 INFO @ Fri, 05 Jul 2019 11:01:35: 19000000 INFO @ Fri, 05 Jul 2019 11:01:38: 21000000 INFO @ Fri, 05 Jul 2019 11:01:40: 17000000 INFO @ Fri, 05 Jul 2019 11:01:43: 20000000 INFO @ Fri, 05 Jul 2019 11:01:46: 22000000 INFO @ Fri, 05 Jul 2019 11:01:50: 18000000 INFO @ Fri, 05 Jul 2019 11:01:52: 21000000 INFO @ Fri, 05 Jul 2019 11:01:54: 23000000 INFO @ Fri, 05 Jul 2019 11:01:59: 19000000 INFO @ Fri, 05 Jul 2019 11:02:01: 22000000 INFO @ Fri, 05 Jul 2019 11:02:02: 24000000 INFO @ Fri, 05 Jul 2019 11:02:09: 20000000 INFO @ Fri, 05 Jul 2019 11:02:09: 25000000 INFO @ Fri, 05 Jul 2019 11:02:09: 23000000 INFO @ Fri, 05 Jul 2019 11:02:17: 26000000 INFO @ Fri, 05 Jul 2019 11:02:18: 24000000 INFO @ Fri, 05 Jul 2019 11:02:19: 21000000 INFO @ Fri, 05 Jul 2019 11:02:25: 27000000 INFO @ Fri, 05 Jul 2019 11:02:26: 25000000 INFO @ Fri, 05 Jul 2019 11:02:29: 22000000 INFO @ Fri, 05 Jul 2019 11:02:33: 28000000 INFO @ Fri, 05 Jul 2019 11:02:35: 26000000 INFO @ Fri, 05 Jul 2019 11:02:39: 23000000 INFO @ Fri, 05 Jul 2019 11:02:41: 29000000 INFO @ Fri, 05 Jul 2019 11:02:43: 27000000 INFO @ Fri, 05 Jul 2019 11:02:49: 30000000 INFO @ Fri, 05 Jul 2019 11:02:49: 24000000 INFO @ Fri, 05 Jul 2019 11:02:51: 28000000 INFO @ Fri, 05 Jul 2019 11:02:56: 31000000 INFO @ Fri, 05 Jul 2019 11:02:58: 25000000 INFO @ Fri, 05 Jul 2019 11:03:00: 29000000 INFO @ Fri, 05 Jul 2019 11:03:04: 32000000 INFO @ Fri, 05 Jul 2019 11:03:08: 26000000 INFO @ Fri, 05 Jul 2019 11:03:08: 30000000 INFO @ Fri, 05 Jul 2019 11:03:12: 33000000 INFO @ Fri, 05 Jul 2019 11:03:17: 31000000 INFO @ Fri, 05 Jul 2019 11:03:17: 27000000 INFO @ Fri, 05 Jul 2019 11:03:20: 34000000 INFO @ Fri, 05 Jul 2019 11:03:25: 32000000 INFO @ Fri, 05 Jul 2019 11:03:27: 28000000 INFO @ Fri, 05 Jul 2019 11:03:28: 35000000 INFO @ Fri, 05 Jul 2019 11:03:34: 33000000 INFO @ Fri, 05 Jul 2019 11:03:35: 36000000 INFO @ Fri, 05 Jul 2019 11:03:36: 29000000 INFO @ Fri, 05 Jul 2019 11:03:42: 34000000 INFO @ Fri, 05 Jul 2019 11:03:43: 37000000 INFO @ Fri, 05 Jul 2019 11:03:46: 30000000 INFO @ Fri, 05 Jul 2019 11:03:51: 38000000 INFO @ Fri, 05 Jul 2019 11:03:51: 35000000 INFO @ Fri, 05 Jul 2019 11:03:55: 31000000 INFO @ Fri, 05 Jul 2019 11:03:58: 39000000 INFO @ Fri, 05 Jul 2019 11:03:59: 36000000 INFO @ Fri, 05 Jul 2019 11:04:04: 32000000 INFO @ Fri, 05 Jul 2019 11:04:06: 40000000 INFO @ Fri, 05 Jul 2019 11:04:07: 37000000 INFO @ Fri, 05 Jul 2019 11:04:14: 41000000 INFO @ Fri, 05 Jul 2019 11:04:14: 33000000 INFO @ Fri, 05 Jul 2019 11:04:16: 38000000 INFO @ Fri, 05 Jul 2019 11:04:21: 42000000 INFO @ Fri, 05 Jul 2019 11:04:23: 34000000 INFO @ Fri, 05 Jul 2019 11:04:24: 39000000 INFO @ Fri, 05 Jul 2019 11:04:29: 43000000 INFO @ Fri, 05 Jul 2019 11:04:33: 40000000 INFO @ Fri, 05 Jul 2019 11:04:33: 35000000 INFO @ Fri, 05 Jul 2019 11:04:36: 44000000 INFO @ Fri, 05 Jul 2019 11:04:41: 41000000 INFO @ Fri, 05 Jul 2019 11:04:42: 36000000 INFO @ Fri, 05 Jul 2019 11:04:44: 45000000 INFO @ Fri, 05 Jul 2019 11:04:49: 42000000 INFO @ Fri, 05 Jul 2019 11:04:52: 37000000 INFO @ Fri, 05 Jul 2019 11:04:52: 46000000 INFO @ Fri, 05 Jul 2019 11:04:58: 43000000 INFO @ Fri, 05 Jul 2019 11:04:59: 47000000 INFO @ Fri, 05 Jul 2019 11:05:01: 38000000 INFO @ Fri, 05 Jul 2019 11:05:06: 44000000 INFO @ Fri, 05 Jul 2019 11:05:07: 48000000 INFO @ Fri, 05 Jul 2019 11:05:11: 39000000 INFO @ Fri, 05 Jul 2019 11:05:14: 45000000 INFO @ Fri, 05 Jul 2019 11:05:15: 49000000 INFO @ Fri, 05 Jul 2019 11:05:20: 40000000 INFO @ Fri, 05 Jul 2019 11:05:22: 50000000 INFO @ Fri, 05 Jul 2019 11:05:23: 46000000 INFO @ Fri, 05 Jul 2019 11:05:30: 41000000 INFO @ Fri, 05 Jul 2019 11:05:30: 51000000 INFO @ Fri, 05 Jul 2019 11:05:31: 47000000 INFO @ Fri, 05 Jul 2019 11:05:38: 52000000 INFO @ Fri, 05 Jul 2019 11:05:39: 42000000 INFO @ Fri, 05 Jul 2019 11:05:40: 48000000 INFO @ Fri, 05 Jul 2019 11:05:46: 53000000 INFO @ Fri, 05 Jul 2019 11:05:48: 49000000 INFO @ Fri, 05 Jul 2019 11:05:48: 43000000 INFO @ Fri, 05 Jul 2019 11:05:51: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:05:51: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:05:51: #1 total tags in treatment: 53562056 INFO @ Fri, 05 Jul 2019 11:05:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:05:51: #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 11:05:52: #1 tags after filtering in treatment: 53561926 INFO @ Fri, 05 Jul 2019 11:05:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:05:52: #1 finished! INFO @ Fri, 05 Jul 2019 11:05:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:05:56: 50000000 INFO @ Fri, 05 Jul 2019 11:05:58: 44000000 INFO @ Fri, 05 Jul 2019 11:06:05: #2 number of paired peaks: 120412 INFO @ Fri, 05 Jul 2019 11:06:05: start model_add_line... INFO @ Fri, 05 Jul 2019 11:06:05: 51000000 INFO @ Fri, 05 Jul 2019 11:06:06: start X-correlation... INFO @ Fri, 05 Jul 2019 11:06:06: end of X-cor INFO @ Fri, 05 Jul 2019 11:06:06: #2 finished! INFO @ Fri, 05 Jul 2019 11:06:06: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 11:06:06: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 05 Jul 2019 11:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.05_model.r INFO @ Fri, 05 Jul 2019 11:06:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:06:07: 45000000 INFO @ Fri, 05 Jul 2019 11:06:13: 52000000 INFO @ Fri, 05 Jul 2019 11:06:16: 46000000 INFO @ Fri, 05 Jul 2019 11:06:21: 53000000 INFO @ Fri, 05 Jul 2019 11:06:26: 47000000 INFO @ Fri, 05 Jul 2019 11:06:27: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:06:27: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:06:27: #1 total tags in treatment: 53562056 INFO @ Fri, 05 Jul 2019 11:06:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:06:27: #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 11:06:28: #1 tags after filtering in treatment: 53561926 INFO @ Fri, 05 Jul 2019 11:06:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:06:28: #1 finished! INFO @ Fri, 05 Jul 2019 11:06:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:06:35: 48000000 INFO @ Fri, 05 Jul 2019 11:06:40: #2 number of paired peaks: 120412 INFO @ Fri, 05 Jul 2019 11:06:40: start model_add_line... INFO @ Fri, 05 Jul 2019 11:06:41: start X-correlation... INFO @ Fri, 05 Jul 2019 11:06:41: end of X-cor INFO @ Fri, 05 Jul 2019 11:06:41: #2 finished! INFO @ Fri, 05 Jul 2019 11:06:41: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 11:06:41: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 05 Jul 2019 11:06:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.10_model.r INFO @ Fri, 05 Jul 2019 11:06:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:06:44: 49000000 INFO @ Fri, 05 Jul 2019 11:06:53: 50000000 INFO @ Fri, 05 Jul 2019 11:07:03: 51000000 INFO @ Fri, 05 Jul 2019 11:07:12: 52000000 INFO @ Fri, 05 Jul 2019 11:07:21: 53000000 INFO @ Fri, 05 Jul 2019 11:07:27: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 11:07:27: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 11:07:27: #1 total tags in treatment: 53562056 INFO @ Fri, 05 Jul 2019 11:07:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:07:27: #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 11:07:29: #1 tags after filtering in treatment: 53561926 INFO @ Fri, 05 Jul 2019 11:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:07:29: #1 finished! INFO @ Fri, 05 Jul 2019 11:07:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:07:40: #2 number of paired peaks: 120412 INFO @ Fri, 05 Jul 2019 11:07:40: start model_add_line... INFO @ Fri, 05 Jul 2019 11:07:41: start X-correlation... INFO @ Fri, 05 Jul 2019 11:07:41: end of X-cor INFO @ Fri, 05 Jul 2019 11:07:41: #2 finished! INFO @ Fri, 05 Jul 2019 11:07:41: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 11:07:41: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 05 Jul 2019 11:07:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.20_model.r INFO @ Fri, 05 Jul 2019 11:07:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:09:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:09:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:10:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:10:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:10:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.05_summits.bed INFO @ Fri, 05 Jul 2019 11:10:41: Done! pass1 - making usageList (165 chroms): 21 millis pass2 - checking and writing primary data (72020 records, 4 fields): 97 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.10_summits.bed INFO @ Fri, 05 Jul 2019 11:11:15: Done! pass1 - making usageList (91 chroms): 7 millis pass2 - checking and writing primary data (20364 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102007/ERX102007.20_summits.bed INFO @ Fri, 05 Jul 2019 11:12:07: Done! pass1 - making usageList (42 chroms): 3 millis pass2 - checking and writing primary data (3152 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。