Job ID = 4178512 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:41:38 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 ) 2019-12-05T03:44:05 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 : 25,164,570 reads read : 25,164,570 reads written : 25,164,570 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:32 25164570 reads; of these: 25164570 (100.00%) were unpaired; of these: 2477542 (9.85%) aligned 0 times 17557110 (69.77%) aligned exactly 1 time 5129918 (20.39%) aligned >1 times 90.15% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8054714 / 22687028 = 0.3550 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:57:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.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 @ Thu, 05 Dec 2019 12:57:16: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:57:16: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:57:21: 1000000 INFO @ Thu, 05 Dec 2019 12:57:26: 2000000 INFO @ Thu, 05 Dec 2019 12:57:31: 3000000 INFO @ Thu, 05 Dec 2019 12:57:36: 4000000 INFO @ Thu, 05 Dec 2019 12:57:41: 5000000 INFO @ Thu, 05 Dec 2019 12:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.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 @ Thu, 05 Dec 2019 12:57:46: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:57:46: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:57:46: 6000000 INFO @ Thu, 05 Dec 2019 12:57:51: 1000000 INFO @ Thu, 05 Dec 2019 12:57:52: 7000000 INFO @ Thu, 05 Dec 2019 12:57:57: 2000000 INFO @ Thu, 05 Dec 2019 12:57:57: 8000000 INFO @ Thu, 05 Dec 2019 12:58:03: 3000000 INFO @ Thu, 05 Dec 2019 12:58:03: 9000000 INFO @ Thu, 05 Dec 2019 12:58:09: 4000000 INFO @ Thu, 05 Dec 2019 12:58:09: 10000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:58:14: 5000000 INFO @ Thu, 05 Dec 2019 12:58:15: 11000000 INFO @ Thu, 05 Dec 2019 12:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.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 @ Thu, 05 Dec 2019 12:58:16: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:58:16: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:58:20: 6000000 INFO @ Thu, 05 Dec 2019 12:58:21: 12000000 INFO @ Thu, 05 Dec 2019 12:58:22: 1000000 INFO @ Thu, 05 Dec 2019 12:58:26: 7000000 INFO @ Thu, 05 Dec 2019 12:58:27: 2000000 INFO @ Thu, 05 Dec 2019 12:58:27: 13000000 INFO @ Thu, 05 Dec 2019 12:58:32: 3000000 INFO @ Thu, 05 Dec 2019 12:58:32: 8000000 INFO @ Thu, 05 Dec 2019 12:58:33: 14000000 INFO @ Thu, 05 Dec 2019 12:58:36: 4000000 INFO @ Thu, 05 Dec 2019 12:58:36: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:58:36: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:58:36: #1 total tags in treatment: 14632314 INFO @ Thu, 05 Dec 2019 12:58:36: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:58:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:58:37: #1 tags after filtering in treatment: 14632314 INFO @ Thu, 05 Dec 2019 12:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:58:37: #1 finished! INFO @ Thu, 05 Dec 2019 12:58:37: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:58:38: #2 number of paired peaks: 1408 INFO @ Thu, 05 Dec 2019 12:58:38: start model_add_line... INFO @ Thu, 05 Dec 2019 12:58:38: start X-correlation... INFO @ Thu, 05 Dec 2019 12:58:38: end of X-cor INFO @ Thu, 05 Dec 2019 12:58:38: #2 finished! INFO @ Thu, 05 Dec 2019 12:58:38: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 12:58:38: #2 alternative fragment length(s) may be 0,22,42,44,70,110,129,151,169,260,287,418,531,565 bps INFO @ Thu, 05 Dec 2019 12:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.05_model.r WARNING @ Thu, 05 Dec 2019 12:58:38: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:58:38: #2 You may need to consider one of the other alternative d(s): 0,22,42,44,70,110,129,151,169,260,287,418,531,565 WARNING @ Thu, 05 Dec 2019 12:58:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:58:38: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:58:38: 9000000 INFO @ Thu, 05 Dec 2019 12:58:41: 5000000 INFO @ Thu, 05 Dec 2019 12:58:44: 10000000 INFO @ Thu, 05 Dec 2019 12:58:46: 6000000 INFO @ Thu, 05 Dec 2019 12:58:50: 11000000 INFO @ Thu, 05 Dec 2019 12:58:51: 7000000 INFO @ Thu, 05 Dec 2019 12:58:55: 12000000 INFO @ Thu, 05 Dec 2019 12:58:55: 8000000 INFO @ Thu, 05 Dec 2019 12:59:00: 9000000 INFO @ Thu, 05 Dec 2019 12:59:01: 13000000 INFO @ Thu, 05 Dec 2019 12:59:05: 10000000 INFO @ Thu, 05 Dec 2019 12:59:07: 14000000 INFO @ Thu, 05 Dec 2019 12:59:10: 11000000 INFO @ Thu, 05 Dec 2019 12:59:11: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:11: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:11: #1 total tags in treatment: 14632314 INFO @ Thu, 05 Dec 2019 12:59:11: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:59:11: #1 tags after filtering in treatment: 14632314 INFO @ Thu, 05 Dec 2019 12:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:11: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:11: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:12: #2 number of paired peaks: 1408 INFO @ Thu, 05 Dec 2019 12:59:12: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:12: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:12: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:12: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:12: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 12:59:12: #2 alternative fragment length(s) may be 0,22,42,44,70,110,129,151,169,260,287,418,531,565 bps INFO @ Thu, 05 Dec 2019 12:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.10_model.r WARNING @ Thu, 05 Dec 2019 12:59:12: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:59:12: #2 You may need to consider one of the other alternative d(s): 0,22,42,44,70,110,129,151,169,260,287,418,531,565 WARNING @ Thu, 05 Dec 2019 12:59:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:59:12: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:59:15: 12000000 INFO @ Thu, 05 Dec 2019 12:59:19: 13000000 INFO @ Thu, 05 Dec 2019 12:59:24: 14000000 INFO @ Thu, 05 Dec 2019 12:59:27: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:59:27: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:59:27: #1 total tags in treatment: 14632314 INFO @ Thu, 05 Dec 2019 12:59:27: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:59:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:59:27: #1 tags after filtering in treatment: 14632314 INFO @ Thu, 05 Dec 2019 12:59:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:59:27: #1 finished! INFO @ Thu, 05 Dec 2019 12:59:27: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:59:28: #2 number of paired peaks: 1408 INFO @ Thu, 05 Dec 2019 12:59:28: start model_add_line... INFO @ Thu, 05 Dec 2019 12:59:28: start X-correlation... INFO @ Thu, 05 Dec 2019 12:59:28: end of X-cor INFO @ Thu, 05 Dec 2019 12:59:28: #2 finished! INFO @ Thu, 05 Dec 2019 12:59:28: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 12:59:28: #2 alternative fragment length(s) may be 0,22,42,44,70,110,129,151,169,260,287,418,531,565 bps INFO @ Thu, 05 Dec 2019 12:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717034/SRX5717034.20_model.r WARNING @ Thu, 05 Dec 2019 12:59:28: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:59:28: #2 You may need to consider one of the other alternative d(s): 0,22,42,44,70,110,129,151,169,260,287,418,531,565 WARNING @ Thu, 05 Dec 2019 12:59:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:59:28: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:59:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/it013/job_scripts/4178512: line 336: 31114 Terminated MACS $i /var/spool/uge/it013/job_scripts/4178512: line 336: 31420 Terminated MACS $i /var/spool/uge/it013/job_scripts/4178512: line 336: 31692 Terminated MACS $i ls: cannot access SRX5717034.05.bed: No such file or directory mv: cannot stat ‘SRX5717034.05.bed’: No such file or directory mv: cannot stat ‘SRX5717034.05.bb’: No such file or directory ls: cannot access SRX5717034.10.bed: No such file or directory mv: cannot stat ‘SRX5717034.10.bed’: No such file or directory mv: cannot stat ‘SRX5717034.10.bb’: No such file or directory ls: cannot access SRX5717034.20.bed: No such file or directory mv: cannot stat ‘SRX5717034.20.bed’: No such file or directory mv: cannot stat ‘SRX5717034.20.bb’: No such file or directory