Job ID = 1294355 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T21:44:38 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 ) 2019-06-02T21:44:38 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 ) 2019-06-02T21:52:56 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 ) 2019-06-02T21:52:56 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 : 21,426,101 reads read : 42,852,202 reads written : 42,852,202 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:47:33 21426101 reads; of these: 21426101 (100.00%) were paired; of these: 2836730 (13.24%) aligned concordantly 0 times 14429349 (67.34%) aligned concordantly exactly 1 time 4160022 (19.42%) aligned concordantly >1 times ---- 2836730 pairs aligned concordantly 0 times; of these: 638030 (22.49%) aligned discordantly 1 time ---- 2198700 pairs aligned 0 times concordantly or discordantly; of these: 4397400 mates make up the pairs; of these: 3114944 (70.84%) aligned 0 times 635025 (14.44%) aligned exactly 1 time 647431 (14.72%) aligned >1 times 92.73% overall alignment rate Time searching: 00:47:34 Overall time: 00:47:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4009180 / 19189903 = 0.2089 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 @ Mon, 03 Jun 2019 08:00:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 08:00:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 08:00:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 08:00:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:44: 1000000 INFO @ Mon, 03 Jun 2019 08:00:46: 1000000 INFO @ Mon, 03 Jun 2019 08:00:46: 1000000 INFO @ Mon, 03 Jun 2019 08:00:53: 2000000 INFO @ Mon, 03 Jun 2019 08:00:56: 2000000 INFO @ Mon, 03 Jun 2019 08:00:57: 2000000 INFO @ Mon, 03 Jun 2019 08:01:02: 3000000 INFO @ Mon, 03 Jun 2019 08:01:07: 3000000 INFO @ Mon, 03 Jun 2019 08:01:08: 3000000 INFO @ Mon, 03 Jun 2019 08:01:10: 4000000 INFO @ Mon, 03 Jun 2019 08:01:17: 4000000 INFO @ Mon, 03 Jun 2019 08:01:18: 5000000 INFO @ Mon, 03 Jun 2019 08:01:19: 4000000 INFO @ Mon, 03 Jun 2019 08:01:27: 6000000 INFO @ Mon, 03 Jun 2019 08:01:27: 5000000 INFO @ Mon, 03 Jun 2019 08:01:29: 5000000 INFO @ Mon, 03 Jun 2019 08:01:35: 7000000 INFO @ Mon, 03 Jun 2019 08:01:38: 6000000 INFO @ Mon, 03 Jun 2019 08:01:40: 6000000 INFO @ Mon, 03 Jun 2019 08:01:43: 8000000 INFO @ Mon, 03 Jun 2019 08:01:48: 7000000 INFO @ Mon, 03 Jun 2019 08:01:51: 7000000 INFO @ Mon, 03 Jun 2019 08:01:52: 9000000 INFO @ Mon, 03 Jun 2019 08:01:58: 8000000 INFO @ Mon, 03 Jun 2019 08:02:00: 10000000 INFO @ Mon, 03 Jun 2019 08:02:01: 8000000 INFO @ Mon, 03 Jun 2019 08:02:09: 11000000 INFO @ Mon, 03 Jun 2019 08:02:09: 9000000 INFO @ Mon, 03 Jun 2019 08:02:12: 9000000 INFO @ Mon, 03 Jun 2019 08:02:17: 12000000 INFO @ Mon, 03 Jun 2019 08:02:20: 10000000 INFO @ Mon, 03 Jun 2019 08:02:23: 10000000 INFO @ Mon, 03 Jun 2019 08:02:27: 13000000 INFO @ Mon, 03 Jun 2019 08:02:31: 11000000 INFO @ Mon, 03 Jun 2019 08:02:34: 11000000 INFO @ Mon, 03 Jun 2019 08:02:37: 14000000 INFO @ Mon, 03 Jun 2019 08:02:42: 12000000 INFO @ Mon, 03 Jun 2019 08:02:45: 15000000 INFO @ Mon, 03 Jun 2019 08:02:45: 12000000 INFO @ Mon, 03 Jun 2019 08:02:52: 13000000 INFO @ Mon, 03 Jun 2019 08:02:52: 16000000 INFO @ Mon, 03 Jun 2019 08:02:55: 13000000 INFO @ Mon, 03 Jun 2019 08:03:00: 17000000 INFO @ Mon, 03 Jun 2019 08:03:02: 14000000 INFO @ Mon, 03 Jun 2019 08:03:06: 14000000 INFO @ Mon, 03 Jun 2019 08:03:08: 18000000 INFO @ Mon, 03 Jun 2019 08:03:13: 15000000 INFO @ Mon, 03 Jun 2019 08:03:16: 19000000 INFO @ Mon, 03 Jun 2019 08:03:16: 15000000 INFO @ Mon, 03 Jun 2019 08:03:23: 16000000 INFO @ Mon, 03 Jun 2019 08:03:23: 20000000 INFO @ Mon, 03 Jun 2019 08:03:27: 16000000 INFO @ Mon, 03 Jun 2019 08:03:31: 21000000 INFO @ Mon, 03 Jun 2019 08:03:34: 17000000 INFO @ Mon, 03 Jun 2019 08:03:37: 17000000 INFO @ Mon, 03 Jun 2019 08:03:39: 22000000 INFO @ Mon, 03 Jun 2019 08:03:44: 18000000 INFO @ Mon, 03 Jun 2019 08:03:46: 23000000 INFO @ Mon, 03 Jun 2019 08:03:48: 18000000 INFO @ Mon, 03 Jun 2019 08:03:54: 24000000 INFO @ Mon, 03 Jun 2019 08:03:54: 19000000 INFO @ Mon, 03 Jun 2019 08:03:59: 19000000 INFO @ Mon, 03 Jun 2019 08:04:02: 25000000 INFO @ Mon, 03 Jun 2019 08:04:05: 20000000 INFO @ Mon, 03 Jun 2019 08:04:11: 26000000 INFO @ Mon, 03 Jun 2019 08:04:12: 20000000 INFO @ Mon, 03 Jun 2019 08:04:16: 21000000 INFO @ Mon, 03 Jun 2019 08:04:20: 27000000 INFO @ Mon, 03 Jun 2019 08:04:25: 21000000 INFO @ Mon, 03 Jun 2019 08:04:26: 22000000 INFO @ Mon, 03 Jun 2019 08:04:28: 28000000 INFO @ Mon, 03 Jun 2019 08:04:36: 23000000 INFO @ Mon, 03 Jun 2019 08:04:36: 29000000 INFO @ Mon, 03 Jun 2019 08:04:37: 22000000 INFO @ Mon, 03 Jun 2019 08:04:44: 30000000 INFO @ Mon, 03 Jun 2019 08:04:45: 24000000 INFO @ Mon, 03 Jun 2019 08:04:48: 23000000 INFO @ Mon, 03 Jun 2019 08:04:51: 31000000 INFO @ Mon, 03 Jun 2019 08:04:55: 25000000 INFO @ Mon, 03 Jun 2019 08:04:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:04:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:04:57: #1 total tags in treatment: 14648787 INFO @ Mon, 03 Jun 2019 08:04:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:04:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:04:58: #1 tags after filtering in treatment: 13044679 INFO @ Mon, 03 Jun 2019 08:04:58: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:04:58: #1 finished! INFO @ Mon, 03 Jun 2019 08:04:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:04:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:04:59: #2 number of paired peaks: 2831 INFO @ Mon, 03 Jun 2019 08:04:59: start model_add_line... INFO @ Mon, 03 Jun 2019 08:04:59: start X-correlation... INFO @ Mon, 03 Jun 2019 08:04:59: end of X-cor INFO @ Mon, 03 Jun 2019 08:04:59: #2 finished! INFO @ Mon, 03 Jun 2019 08:04:59: #2 predicted fragment length is 213 bps INFO @ Mon, 03 Jun 2019 08:04:59: #2 alternative fragment length(s) may be 213 bps INFO @ Mon, 03 Jun 2019 08:04:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.10_model.r INFO @ Mon, 03 Jun 2019 08:04:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:04:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:05:00: 24000000 INFO @ Mon, 03 Jun 2019 08:05:04: 26000000 INFO @ Mon, 03 Jun 2019 08:05:12: 25000000 INFO @ Mon, 03 Jun 2019 08:05:14: 27000000 INFO @ Mon, 03 Jun 2019 08:05:23: 26000000 INFO @ Mon, 03 Jun 2019 08:05:23: 28000000 INFO @ Mon, 03 Jun 2019 08:05:33: 29000000 INFO @ Mon, 03 Jun 2019 08:05:35: 27000000 INFO @ Mon, 03 Jun 2019 08:05:43: 30000000 INFO @ Mon, 03 Jun 2019 08:05:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:05:46: 28000000 INFO @ Mon, 03 Jun 2019 08:05:52: 31000000 INFO @ Mon, 03 Jun 2019 08:05:56: 29000000 INFO @ Mon, 03 Jun 2019 08:05:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:05:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:05:59: #1 total tags in treatment: 14648787 INFO @ Mon, 03 Jun 2019 08:05:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:05:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:05:59: #1 tags after filtering in treatment: 13044679 INFO @ Mon, 03 Jun 2019 08:05:59: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:05:59: #1 finished! INFO @ Mon, 03 Jun 2019 08:05:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:05:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:06:01: #2 number of paired peaks: 2831 INFO @ Mon, 03 Jun 2019 08:06:01: start model_add_line... INFO @ Mon, 03 Jun 2019 08:06:01: start X-correlation... INFO @ Mon, 03 Jun 2019 08:06:01: end of X-cor INFO @ Mon, 03 Jun 2019 08:06:01: #2 finished! INFO @ Mon, 03 Jun 2019 08:06:01: #2 predicted fragment length is 213 bps INFO @ Mon, 03 Jun 2019 08:06:01: #2 alternative fragment length(s) may be 213 bps INFO @ Mon, 03 Jun 2019 08:06:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.20_model.r INFO @ Mon, 03 Jun 2019 08:06:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:06:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:06:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:06:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:06:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.10_summits.bed INFO @ Mon, 03 Jun 2019 08:06:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4626 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:06:06: 30000000 INFO @ Mon, 03 Jun 2019 08:06:15: 31000000 INFO @ Mon, 03 Jun 2019 08:06:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:06:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:06:22: #1 total tags in treatment: 14648787 INFO @ Mon, 03 Jun 2019 08:06:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:06:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:06:23: #1 tags after filtering in treatment: 13044679 INFO @ Mon, 03 Jun 2019 08:06:23: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:06:23: #1 finished! INFO @ Mon, 03 Jun 2019 08:06:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:06:24: #2 number of paired peaks: 2831 INFO @ Mon, 03 Jun 2019 08:06:24: start model_add_line... INFO @ Mon, 03 Jun 2019 08:06:24: start X-correlation... INFO @ Mon, 03 Jun 2019 08:06:24: end of X-cor INFO @ Mon, 03 Jun 2019 08:06:24: #2 finished! INFO @ Mon, 03 Jun 2019 08:06:24: #2 predicted fragment length is 213 bps INFO @ Mon, 03 Jun 2019 08:06:24: #2 alternative fragment length(s) may be 213 bps INFO @ Mon, 03 Jun 2019 08:06:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.05_model.r INFO @ Mon, 03 Jun 2019 08:06:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:06:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:06:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:07:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:07:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.20_summits.bed INFO @ Mon, 03 Jun 2019 08:07:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2970 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:07:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:07:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:07:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:07:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612520/SRX2612520.05_summits.bed INFO @ Mon, 03 Jun 2019 08:07:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6485 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。