Job ID = 1293896 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T18:01:51 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 : 41,041,487 reads read : 82,082,974 reads written : 82,082,974 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: 04:14:57 41041487 reads; of these: 41041487 (100.00%) were paired; of these: 3245143 (7.91%) aligned concordantly 0 times 21680659 (52.83%) aligned concordantly exactly 1 time 16115685 (39.27%) aligned concordantly >1 times ---- 3245143 pairs aligned concordantly 0 times; of these: 584532 (18.01%) aligned discordantly 1 time ---- 2660611 pairs aligned 0 times concordantly or discordantly; of these: 5321222 mates make up the pairs; of these: 3761408 (70.69%) aligned 0 times 609482 (11.45%) aligned exactly 1 time 950332 (17.86%) aligned >1 times 95.42% overall alignment rate Time searching: 04:14:57 Overall time: 04:14:57 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 36 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] 21525581 / 38107087 = 0.5649 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 07:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.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 07:56:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:56:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.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 07:56:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:56:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.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 07:56:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:56:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:56:40: 1000000 INFO @ Mon, 03 Jun 2019 07:56:40: 1000000 INFO @ Mon, 03 Jun 2019 07:56:42: 1000000 INFO @ Mon, 03 Jun 2019 07:56:52: 2000000 INFO @ Mon, 03 Jun 2019 07:56:53: 2000000 INFO @ Mon, 03 Jun 2019 07:56:56: 2000000 INFO @ Mon, 03 Jun 2019 07:57:02: 3000000 INFO @ Mon, 03 Jun 2019 07:57:05: 3000000 INFO @ Mon, 03 Jun 2019 07:57:10: 3000000 INFO @ Mon, 03 Jun 2019 07:57:13: 4000000 INFO @ Mon, 03 Jun 2019 07:57:16: 4000000 INFO @ Mon, 03 Jun 2019 07:57:23: 5000000 INFO @ Mon, 03 Jun 2019 07:57:23: 4000000 INFO @ Mon, 03 Jun 2019 07:57:27: 5000000 INFO @ Mon, 03 Jun 2019 07:57:33: 6000000 INFO @ Mon, 03 Jun 2019 07:57:34: 5000000 INFO @ Mon, 03 Jun 2019 07:57:38: 6000000 INFO @ Mon, 03 Jun 2019 07:57:43: 7000000 INFO @ Mon, 03 Jun 2019 07:57:47: 6000000 INFO @ Mon, 03 Jun 2019 07:57:49: 7000000 INFO @ Mon, 03 Jun 2019 07:57:53: 8000000 INFO @ Mon, 03 Jun 2019 07:57:59: 8000000 INFO @ Mon, 03 Jun 2019 07:58:00: 7000000 INFO @ Mon, 03 Jun 2019 07:58:04: 9000000 INFO @ Mon, 03 Jun 2019 07:58:12: 9000000 INFO @ Mon, 03 Jun 2019 07:58:13: 8000000 INFO @ Mon, 03 Jun 2019 07:58:14: 10000000 INFO @ Mon, 03 Jun 2019 07:58:23: 10000000 INFO @ Mon, 03 Jun 2019 07:58:24: 11000000 INFO @ Mon, 03 Jun 2019 07:58:25: 9000000 INFO @ Mon, 03 Jun 2019 07:58:34: 11000000 INFO @ Mon, 03 Jun 2019 07:58:35: 12000000 INFO @ Mon, 03 Jun 2019 07:58:39: 10000000 INFO @ Mon, 03 Jun 2019 07:58:45: 12000000 INFO @ Mon, 03 Jun 2019 07:58:45: 13000000 INFO @ Mon, 03 Jun 2019 07:58:52: 11000000 INFO @ Mon, 03 Jun 2019 07:58:55: 14000000 INFO @ Mon, 03 Jun 2019 07:58:56: 13000000 INFO @ Mon, 03 Jun 2019 07:59:05: 12000000 INFO @ Mon, 03 Jun 2019 07:59:05: 15000000 INFO @ Mon, 03 Jun 2019 07:59:06: 14000000 INFO @ Mon, 03 Jun 2019 07:59:16: 16000000 INFO @ Mon, 03 Jun 2019 07:59:17: 15000000 INFO @ Mon, 03 Jun 2019 07:59:18: 13000000 INFO @ Mon, 03 Jun 2019 07:59:27: 17000000 INFO @ Mon, 03 Jun 2019 07:59:29: 16000000 INFO @ Mon, 03 Jun 2019 07:59:30: 14000000 INFO @ Mon, 03 Jun 2019 07:59:38: 18000000 INFO @ Mon, 03 Jun 2019 07:59:40: 17000000 INFO @ Mon, 03 Jun 2019 07:59:43: 15000000 INFO @ Mon, 03 Jun 2019 07:59:48: 19000000 INFO @ Mon, 03 Jun 2019 07:59:50: 18000000 INFO @ Mon, 03 Jun 2019 07:59:55: 16000000 INFO @ Mon, 03 Jun 2019 07:59:59: 20000000 INFO @ Mon, 03 Jun 2019 08:00:01: 19000000 INFO @ Mon, 03 Jun 2019 08:00:08: 17000000 INFO @ Mon, 03 Jun 2019 08:00:10: 21000000 INFO @ Mon, 03 Jun 2019 08:00:12: 20000000 INFO @ Mon, 03 Jun 2019 08:00:20: 18000000 INFO @ Mon, 03 Jun 2019 08:00:21: 22000000 INFO @ Mon, 03 Jun 2019 08:00:22: 21000000 INFO @ Mon, 03 Jun 2019 08:00:33: 23000000 INFO @ Mon, 03 Jun 2019 08:00:34: 19000000 INFO @ Mon, 03 Jun 2019 08:00:35: 22000000 INFO @ Mon, 03 Jun 2019 08:00:44: 24000000 INFO @ Mon, 03 Jun 2019 08:00:47: 23000000 INFO @ Mon, 03 Jun 2019 08:00:47: 20000000 INFO @ Mon, 03 Jun 2019 08:00:54: 25000000 INFO @ Mon, 03 Jun 2019 08:00:57: 24000000 INFO @ Mon, 03 Jun 2019 08:01:00: 21000000 INFO @ Mon, 03 Jun 2019 08:01:05: 26000000 INFO @ Mon, 03 Jun 2019 08:01:08: 25000000 INFO @ Mon, 03 Jun 2019 08:01:12: 22000000 INFO @ Mon, 03 Jun 2019 08:01:15: 27000000 INFO @ Mon, 03 Jun 2019 08:01:19: 26000000 INFO @ Mon, 03 Jun 2019 08:01:25: 23000000 INFO @ Mon, 03 Jun 2019 08:01:26: 28000000 INFO @ Mon, 03 Jun 2019 08:01:29: 27000000 INFO @ Mon, 03 Jun 2019 08:01:37: 29000000 INFO @ Mon, 03 Jun 2019 08:01:38: 24000000 INFO @ Mon, 03 Jun 2019 08:01:40: 28000000 INFO @ Mon, 03 Jun 2019 08:01:48: 30000000 INFO @ Mon, 03 Jun 2019 08:01:50: 25000000 INFO @ Mon, 03 Jun 2019 08:01:52: 29000000 INFO @ Mon, 03 Jun 2019 08:02:00: 31000000 INFO @ Mon, 03 Jun 2019 08:02:04: 26000000 INFO @ Mon, 03 Jun 2019 08:02:05: 30000000 INFO @ Mon, 03 Jun 2019 08:02:12: 32000000 INFO @ Mon, 03 Jun 2019 08:02:16: 27000000 INFO @ Mon, 03 Jun 2019 08:02:16: 31000000 INFO @ Mon, 03 Jun 2019 08:02:22: 33000000 INFO @ Mon, 03 Jun 2019 08:02:28: 32000000 INFO @ Mon, 03 Jun 2019 08:02:29: 28000000 INFO @ Mon, 03 Jun 2019 08:02:32: 34000000 INFO @ Mon, 03 Jun 2019 08:02:38: 33000000 INFO @ Mon, 03 Jun 2019 08:02:41: 29000000 INFO @ Mon, 03 Jun 2019 08:02:42: 35000000 INFO @ Mon, 03 Jun 2019 08:02:45: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 08:02:45: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 08:02:45: #1 total tags in treatment: 16577687 INFO @ Mon, 03 Jun 2019 08:02:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:02:45: #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 08:02:45: #1 tags after filtering in treatment: 12989782 INFO @ Mon, 03 Jun 2019 08:02:45: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 08:02:45: #1 finished! INFO @ Mon, 03 Jun 2019 08:02:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:02:47: #2 number of paired peaks: 2810 INFO @ Mon, 03 Jun 2019 08:02:47: start model_add_line... INFO @ Mon, 03 Jun 2019 08:02:47: start X-correlation... INFO @ Mon, 03 Jun 2019 08:02:47: end of X-cor INFO @ Mon, 03 Jun 2019 08:02:47: #2 finished! INFO @ Mon, 03 Jun 2019 08:02:47: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 08:02:47: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 08:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.10_model.r WARNING @ Mon, 03 Jun 2019 08:02:47: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:02:47: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Mon, 03 Jun 2019 08:02:47: #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 08:02:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:02:49: 34000000 INFO @ Mon, 03 Jun 2019 08:02:56: 30000000 INFO @ Mon, 03 Jun 2019 08:02:59: 35000000 INFO @ Mon, 03 Jun 2019 08:03:02: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 08:03:02: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 08:03:02: #1 total tags in treatment: 16577687 INFO @ Mon, 03 Jun 2019 08:03:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:03:02: #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 08:03:02: #1 tags after filtering in treatment: 12989782 INFO @ Mon, 03 Jun 2019 08:03:02: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 08:03:02: #1 finished! INFO @ Mon, 03 Jun 2019 08:03:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:03:04: #2 number of paired peaks: 2810 INFO @ Mon, 03 Jun 2019 08:03:04: start model_add_line... INFO @ Mon, 03 Jun 2019 08:03:04: start X-correlation... INFO @ Mon, 03 Jun 2019 08:03:04: end of X-cor INFO @ Mon, 03 Jun 2019 08:03:04: #2 finished! INFO @ Mon, 03 Jun 2019 08:03:04: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 08:03:04: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 08:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.20_model.r WARNING @ Mon, 03 Jun 2019 08:03:04: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:03:04: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Mon, 03 Jun 2019 08:03:04: #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 08:03:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:03:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:03:10: 31000000 INFO @ Mon, 03 Jun 2019 08:03:24: 32000000 INFO @ Mon, 03 Jun 2019 08:03:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:03:38: 33000000 INFO @ Mon, 03 Jun 2019 08:03:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.10_summits.bed INFO @ Mon, 03 Jun 2019 08:03:49: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7764 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:03:53: 34000000 INFO @ Mon, 03 Jun 2019 08:04:04: 35000000 INFO @ Mon, 03 Jun 2019 08:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.20_summits.bed INFO @ Mon, 03 Jun 2019 08:04:06: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4124 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:04:07: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 08:04:07: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 08:04:07: #1 total tags in treatment: 16577687 INFO @ Mon, 03 Jun 2019 08:04:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:04:07: #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 08:04:08: #1 tags after filtering in treatment: 12989782 INFO @ Mon, 03 Jun 2019 08:04:08: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 08:04:08: #1 finished! INFO @ Mon, 03 Jun 2019 08:04:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:04:09: #2 number of paired peaks: 2810 INFO @ Mon, 03 Jun 2019 08:04:09: start model_add_line... INFO @ Mon, 03 Jun 2019 08:04:09: start X-correlation... INFO @ Mon, 03 Jun 2019 08:04:09: end of X-cor INFO @ Mon, 03 Jun 2019 08:04:09: #2 finished! INFO @ Mon, 03 Jun 2019 08:04:09: #2 predicted fragment length is 143 bps INFO @ Mon, 03 Jun 2019 08:04:09: #2 alternative fragment length(s) may be 143 bps INFO @ Mon, 03 Jun 2019 08:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.05_model.r WARNING @ Mon, 03 Jun 2019 08:04:09: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:04:09: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Mon, 03 Jun 2019 08:04:09: #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 08:04:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:04:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:05:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:05:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:05:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146993/SRX146993.05_summits.bed INFO @ Mon, 03 Jun 2019 08:05:12: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (11523 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。