Job ID = 1293413 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T15:02:55 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 ) 2019-06-02T15:13:55 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 ) 2019-06-02T15:13:55 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 : 26,494,398 reads read : 52,988,796 reads written : 52,988,796 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:13:43 26494398 reads; of these: 26494398 (100.00%) were paired; of these: 8497320 (32.07%) aligned concordantly 0 times 13345482 (50.37%) aligned concordantly exactly 1 time 4651596 (17.56%) aligned concordantly >1 times ---- 8497320 pairs aligned concordantly 0 times; of these: 3178398 (37.40%) aligned discordantly 1 time ---- 5318922 pairs aligned 0 times concordantly or discordantly; of these: 10637844 mates make up the pairs; of these: 8014834 (75.34%) aligned 0 times 517085 (4.86%) aligned exactly 1 time 2105925 (19.80%) aligned >1 times 84.87% overall alignment rate Time searching: 01:13:43 Overall time: 01:13:43 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 28 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] 6845920 / 20919489 = 0.3273 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 01:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.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 01:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.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 01:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.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 01:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:58:34: 1000000 INFO @ Mon, 03 Jun 2019 01:58:36: 1000000 INFO @ Mon, 03 Jun 2019 01:58:40: 1000000 INFO @ Mon, 03 Jun 2019 01:58:48: 2000000 INFO @ Mon, 03 Jun 2019 01:58:50: 2000000 INFO @ Mon, 03 Jun 2019 01:58:58: 2000000 INFO @ Mon, 03 Jun 2019 01:59:02: 3000000 INFO @ Mon, 03 Jun 2019 01:59:04: 3000000 INFO @ Mon, 03 Jun 2019 01:59:15: 4000000 INFO @ Mon, 03 Jun 2019 01:59:16: 3000000 INFO @ Mon, 03 Jun 2019 01:59:17: 4000000 INFO @ Mon, 03 Jun 2019 01:59:29: 5000000 INFO @ Mon, 03 Jun 2019 01:59:31: 5000000 INFO @ Mon, 03 Jun 2019 01:59:33: 4000000 INFO @ Mon, 03 Jun 2019 01:59:42: 6000000 INFO @ Mon, 03 Jun 2019 01:59:45: 6000000 INFO @ Mon, 03 Jun 2019 01:59:47: 5000000 INFO @ Mon, 03 Jun 2019 01:59:56: 7000000 INFO @ Mon, 03 Jun 2019 01:59:59: 7000000 INFO @ Mon, 03 Jun 2019 02:00:03: 6000000 INFO @ Mon, 03 Jun 2019 02:00:10: 8000000 INFO @ Mon, 03 Jun 2019 02:00:13: 8000000 INFO @ Mon, 03 Jun 2019 02:00:19: 7000000 INFO @ Mon, 03 Jun 2019 02:00:23: 9000000 INFO @ Mon, 03 Jun 2019 02:00:25: 9000000 INFO @ Mon, 03 Jun 2019 02:00:33: 8000000 INFO @ Mon, 03 Jun 2019 02:00:37: 10000000 INFO @ Mon, 03 Jun 2019 02:00:37: 10000000 INFO @ Mon, 03 Jun 2019 02:00:47: 9000000 INFO @ Mon, 03 Jun 2019 02:00:50: 11000000 INFO @ Mon, 03 Jun 2019 02:00:50: 11000000 INFO @ Mon, 03 Jun 2019 02:01:01: 10000000 INFO @ Mon, 03 Jun 2019 02:01:02: 12000000 INFO @ Mon, 03 Jun 2019 02:01:03: 12000000 INFO @ Mon, 03 Jun 2019 02:01:13: 13000000 INFO @ Mon, 03 Jun 2019 02:01:15: 11000000 INFO @ Mon, 03 Jun 2019 02:01:15: 13000000 INFO @ Mon, 03 Jun 2019 02:01:24: 14000000 INFO @ Mon, 03 Jun 2019 02:01:27: 14000000 INFO @ Mon, 03 Jun 2019 02:01:28: 12000000 INFO @ Mon, 03 Jun 2019 02:01:36: 15000000 INFO @ Mon, 03 Jun 2019 02:01:39: 15000000 INFO @ Mon, 03 Jun 2019 02:01:42: 13000000 INFO @ Mon, 03 Jun 2019 02:01:47: 16000000 INFO @ Mon, 03 Jun 2019 02:01:51: 16000000 INFO @ Mon, 03 Jun 2019 02:01:55: 14000000 INFO @ Mon, 03 Jun 2019 02:01:58: 17000000 INFO @ Mon, 03 Jun 2019 02:02:03: 17000000 INFO @ Mon, 03 Jun 2019 02:02:09: 15000000 INFO @ Mon, 03 Jun 2019 02:02:09: 18000000 INFO @ Mon, 03 Jun 2019 02:02:16: 18000000 INFO @ Mon, 03 Jun 2019 02:02:20: 19000000 INFO @ Mon, 03 Jun 2019 02:02:22: 16000000 INFO @ Mon, 03 Jun 2019 02:02:28: 19000000 INFO @ Mon, 03 Jun 2019 02:02:32: 20000000 INFO @ Mon, 03 Jun 2019 02:02:36: 17000000 INFO @ Mon, 03 Jun 2019 02:02:40: 20000000 INFO @ Mon, 03 Jun 2019 02:02:45: 21000000 INFO @ Mon, 03 Jun 2019 02:02:49: 18000000 INFO @ Mon, 03 Jun 2019 02:02:52: 21000000 INFO @ Mon, 03 Jun 2019 02:02:57: 22000000 INFO @ Mon, 03 Jun 2019 02:03:02: 19000000 INFO @ Mon, 03 Jun 2019 02:03:04: 22000000 INFO @ Mon, 03 Jun 2019 02:03:09: 23000000 INFO @ Mon, 03 Jun 2019 02:03:16: 23000000 INFO @ Mon, 03 Jun 2019 02:03:16: 20000000 INFO @ Mon, 03 Jun 2019 02:03:22: 24000000 INFO @ Mon, 03 Jun 2019 02:03:28: 24000000 INFO @ Mon, 03 Jun 2019 02:03:29: 21000000 INFO @ Mon, 03 Jun 2019 02:03:35: 25000000 INFO @ Mon, 03 Jun 2019 02:03:41: 25000000 INFO @ Mon, 03 Jun 2019 02:03:42: 22000000 INFO @ Mon, 03 Jun 2019 02:03:48: 26000000 INFO @ Mon, 03 Jun 2019 02:03:53: 26000000 INFO @ Mon, 03 Jun 2019 02:03:56: 23000000 INFO @ Mon, 03 Jun 2019 02:04:01: 27000000 INFO @ Mon, 03 Jun 2019 02:04:05: 27000000 INFO @ Mon, 03 Jun 2019 02:04:09: 24000000 INFO @ Mon, 03 Jun 2019 02:04:13: 28000000 INFO @ Mon, 03 Jun 2019 02:04:17: 28000000 INFO @ Mon, 03 Jun 2019 02:04:22: 25000000 INFO @ Mon, 03 Jun 2019 02:04:26: 29000000 INFO @ Mon, 03 Jun 2019 02:04:29: 29000000 INFO @ Mon, 03 Jun 2019 02:04:35: 26000000 INFO @ Mon, 03 Jun 2019 02:04:37: 30000000 INFO @ Mon, 03 Jun 2019 02:04:40: 30000000 INFO @ Mon, 03 Jun 2019 02:04:47: 31000000 INFO @ Mon, 03 Jun 2019 02:04:48: 27000000 INFO @ Mon, 03 Jun 2019 02:04:49: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:04:49: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:04:49: #1 total tags in treatment: 12061766 INFO @ Mon, 03 Jun 2019 02:04:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:04:49: #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 02:04:50: #1 tags after filtering in treatment: 9524227 INFO @ Mon, 03 Jun 2019 02:04:50: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 02:04:50: #1 finished! INFO @ Mon, 03 Jun 2019 02:04:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:04:50: 31000000 INFO @ Mon, 03 Jun 2019 02:04:51: #2 number of paired peaks: 3096 INFO @ Mon, 03 Jun 2019 02:04:51: start model_add_line... INFO @ Mon, 03 Jun 2019 02:04:51: start X-correlation... INFO @ Mon, 03 Jun 2019 02:04:51: end of X-cor INFO @ Mon, 03 Jun 2019 02:04:51: #2 finished! INFO @ Mon, 03 Jun 2019 02:04:51: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 02:04:51: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 02:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.20_model.r WARNING @ Mon, 03 Jun 2019 02:04:51: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:04:51: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 02:04:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:04:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:04:53: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:04:53: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:04:53: #1 total tags in treatment: 12061766 INFO @ Mon, 03 Jun 2019 02:04:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:04:53: #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 02:04:54: #1 tags after filtering in treatment: 9524227 INFO @ Mon, 03 Jun 2019 02:04:54: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 02:04:54: #1 finished! INFO @ Mon, 03 Jun 2019 02:04:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:04:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:04:55: #2 number of paired peaks: 3096 INFO @ Mon, 03 Jun 2019 02:04:55: start model_add_line... INFO @ Mon, 03 Jun 2019 02:04:55: start X-correlation... INFO @ Mon, 03 Jun 2019 02:04:55: end of X-cor INFO @ Mon, 03 Jun 2019 02:04:55: #2 finished! INFO @ Mon, 03 Jun 2019 02:04:55: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 02:04:55: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 02:04:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.10_model.r WARNING @ Mon, 03 Jun 2019 02:04:55: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:04:55: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 02:04:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:04:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:04:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:05:00: 28000000 INFO @ Mon, 03 Jun 2019 02:05:13: 29000000 INFO @ Mon, 03 Jun 2019 02:05:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:05:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:05:26: 30000000 INFO @ Mon, 03 Jun 2019 02:05:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:05:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.20_summits.bed INFO @ Mon, 03 Jun 2019 02:05:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4285 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:05:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:05:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:05:39: 31000000 INFO @ Mon, 03 Jun 2019 02:05:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.10_summits.bed INFO @ Mon, 03 Jun 2019 02:05:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7596 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:05:42: #1 tag size is determined as 121 bps INFO @ Mon, 03 Jun 2019 02:05:42: #1 tag size = 121 INFO @ Mon, 03 Jun 2019 02:05:42: #1 total tags in treatment: 12061766 INFO @ Mon, 03 Jun 2019 02:05:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:05:42: #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 02:05:42: #1 tags after filtering in treatment: 9524227 INFO @ Mon, 03 Jun 2019 02:05:42: #1 Redundant rate of treatment: 0.21 INFO @ Mon, 03 Jun 2019 02:05:42: #1 finished! INFO @ Mon, 03 Jun 2019 02:05:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:05:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:05:44: #2 number of paired peaks: 3096 INFO @ Mon, 03 Jun 2019 02:05:44: start model_add_line... INFO @ Mon, 03 Jun 2019 02:05:44: start X-correlation... INFO @ Mon, 03 Jun 2019 02:05:44: end of X-cor INFO @ Mon, 03 Jun 2019 02:05:44: #2 finished! INFO @ Mon, 03 Jun 2019 02:05:44: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 02:05:44: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 02:05:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.05_model.r WARNING @ Mon, 03 Jun 2019 02:05:44: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:05:44: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Mon, 03 Jun 2019 02:05:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 02:05:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:05:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:06:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 02:06:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:06:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:06:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX2145594/ERX2145594.05_summits.bed INFO @ Mon, 03 Jun 2019 02:06:28: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (11045 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。