Job ID = 5720221 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T12:37:13 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 ) 2020-04-15T12:37:13 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 : 48,056,231 reads read : 96,112,462 reads written : 48,056,231 reads 0-length : 48,056,231 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: 00:10:35 48056231 reads; of these: 48056231 (100.00%) were unpaired; of these: 2563796 (5.33%) aligned 0 times 38466580 (80.04%) aligned exactly 1 time 7025855 (14.62%) aligned >1 times 94.67% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 11181742 / 45492435 = 0.2458 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:10:22: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:10:22: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:10:28: 1000000 INFO @ Wed, 15 Apr 2020 22:10:34: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:10:40: 3000000 INFO @ Wed, 15 Apr 2020 22:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:10:42: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:10:42: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:10:46: 4000000 INFO @ Wed, 15 Apr 2020 22:10:47: 1000000 INFO @ Wed, 15 Apr 2020 22:10:52: 5000000 INFO @ Wed, 15 Apr 2020 22:10:52: 2000000 INFO @ Wed, 15 Apr 2020 22:10:57: 3000000 INFO @ Wed, 15 Apr 2020 22:10:58: 6000000 INFO @ Wed, 15 Apr 2020 22:11:03: 4000000 INFO @ Wed, 15 Apr 2020 22:11:03: 7000000 INFO @ Wed, 15 Apr 2020 22:11:08: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:11:10: 8000000 INFO @ Wed, 15 Apr 2020 22:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 15 Apr 2020 22:11:12: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:11:12: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:11:13: 6000000 INFO @ Wed, 15 Apr 2020 22:11:16: 9000000 INFO @ Wed, 15 Apr 2020 22:11:18: 1000000 INFO @ Wed, 15 Apr 2020 22:11:19: 7000000 INFO @ Wed, 15 Apr 2020 22:11:21: 10000000 INFO @ Wed, 15 Apr 2020 22:11:23: 2000000 INFO @ Wed, 15 Apr 2020 22:11:24: 8000000 INFO @ Wed, 15 Apr 2020 22:11:27: 11000000 INFO @ Wed, 15 Apr 2020 22:11:29: 3000000 INFO @ Wed, 15 Apr 2020 22:11:30: 9000000 INFO @ Wed, 15 Apr 2020 22:11:34: 12000000 INFO @ Wed, 15 Apr 2020 22:11:34: 4000000 INFO @ Wed, 15 Apr 2020 22:11:35: 10000000 INFO @ Wed, 15 Apr 2020 22:11:40: 5000000 INFO @ Wed, 15 Apr 2020 22:11:40: 13000000 INFO @ Wed, 15 Apr 2020 22:11:40: 11000000 INFO @ Wed, 15 Apr 2020 22:11:45: 6000000 INFO @ Wed, 15 Apr 2020 22:11:45: 14000000 INFO @ Wed, 15 Apr 2020 22:11:46: 12000000 INFO @ Wed, 15 Apr 2020 22:11:51: 7000000 INFO @ Wed, 15 Apr 2020 22:11:51: 15000000 INFO @ Wed, 15 Apr 2020 22:11:52: 13000000 INFO @ Wed, 15 Apr 2020 22:11:56: 8000000 INFO @ Wed, 15 Apr 2020 22:11:57: 14000000 INFO @ Wed, 15 Apr 2020 22:11:57: 16000000 INFO @ Wed, 15 Apr 2020 22:12:02: 9000000 INFO @ Wed, 15 Apr 2020 22:12:03: 15000000 INFO @ Wed, 15 Apr 2020 22:12:04: 17000000 INFO @ Wed, 15 Apr 2020 22:12:07: 10000000 INFO @ Wed, 15 Apr 2020 22:12:08: 16000000 INFO @ Wed, 15 Apr 2020 22:12:10: 18000000 INFO @ Wed, 15 Apr 2020 22:12:13: 11000000 INFO @ Wed, 15 Apr 2020 22:12:14: 17000000 INFO @ Wed, 15 Apr 2020 22:12:16: 19000000 INFO @ Wed, 15 Apr 2020 22:12:18: 12000000 INFO @ Wed, 15 Apr 2020 22:12:19: 18000000 INFO @ Wed, 15 Apr 2020 22:12:22: 20000000 INFO @ Wed, 15 Apr 2020 22:12:24: 13000000 INFO @ Wed, 15 Apr 2020 22:12:25: 19000000 INFO @ Wed, 15 Apr 2020 22:12:28: 21000000 INFO @ Wed, 15 Apr 2020 22:12:30: 14000000 INFO @ Wed, 15 Apr 2020 22:12:30: 20000000 INFO @ Wed, 15 Apr 2020 22:12:34: 22000000 INFO @ Wed, 15 Apr 2020 22:12:35: 15000000 INFO @ Wed, 15 Apr 2020 22:12:36: 21000000 INFO @ Wed, 15 Apr 2020 22:12:39: 23000000 INFO @ Wed, 15 Apr 2020 22:12:41: 16000000 INFO @ Wed, 15 Apr 2020 22:12:41: 22000000 INFO @ Wed, 15 Apr 2020 22:12:45: 24000000 INFO @ Wed, 15 Apr 2020 22:12:46: 17000000 INFO @ Wed, 15 Apr 2020 22:12:47: 23000000 INFO @ Wed, 15 Apr 2020 22:12:51: 25000000 INFO @ Wed, 15 Apr 2020 22:12:52: 18000000 INFO @ Wed, 15 Apr 2020 22:12:52: 24000000 INFO @ Wed, 15 Apr 2020 22:12:57: 26000000 INFO @ Wed, 15 Apr 2020 22:12:58: 19000000 INFO @ Wed, 15 Apr 2020 22:12:58: 25000000 INFO @ Wed, 15 Apr 2020 22:13:03: 27000000 INFO @ Wed, 15 Apr 2020 22:13:04: 20000000 INFO @ Wed, 15 Apr 2020 22:13:04: 26000000 INFO @ Wed, 15 Apr 2020 22:13:09: 28000000 INFO @ Wed, 15 Apr 2020 22:13:10: 21000000 INFO @ Wed, 15 Apr 2020 22:13:10: 27000000 INFO @ Wed, 15 Apr 2020 22:13:15: 29000000 INFO @ Wed, 15 Apr 2020 22:13:16: 22000000 INFO @ Wed, 15 Apr 2020 22:13:16: 28000000 INFO @ Wed, 15 Apr 2020 22:13:21: 30000000 INFO @ Wed, 15 Apr 2020 22:13:21: 23000000 INFO @ Wed, 15 Apr 2020 22:13:22: 29000000 INFO @ Wed, 15 Apr 2020 22:13:27: 24000000 INFO @ Wed, 15 Apr 2020 22:13:27: 30000000 INFO @ Wed, 15 Apr 2020 22:13:27: 31000000 INFO @ Wed, 15 Apr 2020 22:13:32: 25000000 INFO @ Wed, 15 Apr 2020 22:13:33: 31000000 INFO @ Wed, 15 Apr 2020 22:13:33: 32000000 INFO @ Wed, 15 Apr 2020 22:13:38: 26000000 INFO @ Wed, 15 Apr 2020 22:13:38: 32000000 INFO @ Wed, 15 Apr 2020 22:13:39: 33000000 INFO @ Wed, 15 Apr 2020 22:13:43: 27000000 INFO @ Wed, 15 Apr 2020 22:13:44: 33000000 INFO @ Wed, 15 Apr 2020 22:13:45: 34000000 INFO @ Wed, 15 Apr 2020 22:13:47: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:13:47: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:13:47: #1 total tags in treatment: 34310693 INFO @ Wed, 15 Apr 2020 22:13:47: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:13:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:13:47: #1 tags after filtering in treatment: 34310693 INFO @ Wed, 15 Apr 2020 22:13:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:13:47: #1 finished! INFO @ Wed, 15 Apr 2020 22:13:47: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:13:49: 28000000 INFO @ Wed, 15 Apr 2020 22:13:49: 34000000 INFO @ Wed, 15 Apr 2020 22:13:50: #2 number of paired peaks: 100 WARNING @ Wed, 15 Apr 2020 22:13:50: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 15 Apr 2020 22:13:50: start model_add_line... INFO @ Wed, 15 Apr 2020 22:13:50: start X-correlation... INFO @ Wed, 15 Apr 2020 22:13:50: end of X-cor INFO @ Wed, 15 Apr 2020 22:13:50: #2 finished! INFO @ Wed, 15 Apr 2020 22:13:50: #2 predicted fragment length is 0 bps INFO @ Wed, 15 Apr 2020 22:13:50: #2 alternative fragment length(s) may be 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 bps INFO @ Wed, 15 Apr 2020 22:13:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.05_model.r WARNING @ Wed, 15 Apr 2020 22:13:50: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:13:50: #2 You may need to consider one of the other alternative d(s): 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 WARNING @ Wed, 15 Apr 2020 22:13:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:13:50: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:13:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:13:51: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:13:51: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:13:51: #1 total tags in treatment: 34310693 INFO @ Wed, 15 Apr 2020 22:13:51: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:13:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:13:52: #1 tags after filtering in treatment: 34310693 INFO @ Wed, 15 Apr 2020 22:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:13:52: #1 finished! INFO @ Wed, 15 Apr 2020 22:13:52: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:13:54: #2 number of paired peaks: 100 WARNING @ Wed, 15 Apr 2020 22:13:54: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 15 Apr 2020 22:13:54: start model_add_line... INFO @ Wed, 15 Apr 2020 22:13:54: start X-correlation... INFO @ Wed, 15 Apr 2020 22:13:54: end of X-cor INFO @ Wed, 15 Apr 2020 22:13:54: #2 finished! INFO @ Wed, 15 Apr 2020 22:13:54: #2 predicted fragment length is 0 bps INFO @ Wed, 15 Apr 2020 22:13:54: #2 alternative fragment length(s) may be 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 bps INFO @ Wed, 15 Apr 2020 22:13:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.10_model.r WARNING @ Wed, 15 Apr 2020 22:13:54: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:13:54: #2 You may need to consider one of the other alternative d(s): 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 WARNING @ Wed, 15 Apr 2020 22:13:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:13:54: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:13:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:13:54: 29000000 INFO @ Wed, 15 Apr 2020 22:13:59: 30000000 INFO @ Wed, 15 Apr 2020 22:14:05: 31000000 INFO @ Wed, 15 Apr 2020 22:14:10: 32000000 INFO @ Wed, 15 Apr 2020 22:14:15: 33000000 INFO @ Wed, 15 Apr 2020 22:14:20: 34000000 INFO @ Wed, 15 Apr 2020 22:14:22: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:14:22: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:14:22: #1 total tags in treatment: 34310693 INFO @ Wed, 15 Apr 2020 22:14:22: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:14:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:14:23: #1 tags after filtering in treatment: 34310693 INFO @ Wed, 15 Apr 2020 22:14:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:14:23: #1 finished! INFO @ Wed, 15 Apr 2020 22:14:23: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:14:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:14:25: #2 number of paired peaks: 100 WARNING @ Wed, 15 Apr 2020 22:14:25: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 15 Apr 2020 22:14:25: start model_add_line... INFO @ Wed, 15 Apr 2020 22:14:25: start X-correlation... INFO @ Wed, 15 Apr 2020 22:14:25: end of X-cor INFO @ Wed, 15 Apr 2020 22:14:25: #2 finished! INFO @ Wed, 15 Apr 2020 22:14:25: #2 predicted fragment length is 0 bps INFO @ Wed, 15 Apr 2020 22:14:25: #2 alternative fragment length(s) may be 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 bps INFO @ Wed, 15 Apr 2020 22:14:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619593/SRX6619593.20_model.r WARNING @ Wed, 15 Apr 2020 22:14:25: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:14:25: #2 You may need to consider one of the other alternative d(s): 0,13,24,49,87,113,132,148,182,208,243,255,257,279,302,326,361,396,408,431,455,507,521,528,582 WARNING @ Wed, 15 Apr 2020 22:14:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:14:25: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:14:25: #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/it018/job_scripts/5720221: line 336: 4972 Terminated MACS $i /var/spool/uge/it018/job_scripts/5720221: line 336: 5067 Terminated MACS $i /var/spool/uge/it018/job_scripts/5720221: line 336: 5153 Terminated MACS $i ls: cannot access SRX6619593.05.bed: No such file or directory mv: cannot stat ‘SRX6619593.05.bed’: No such file or directory mv: cannot stat ‘SRX6619593.05.bb’: No such file or directory ls: cannot access SRX6619593.10.bed: No such file or directory mv: cannot stat ‘SRX6619593.10.bed’: No such file or directory mv: cannot stat ‘SRX6619593.10.bb’: No such file or directory ls: cannot access SRX6619593.20.bed: No such file or directory mv: cannot stat ‘SRX6619593.20.bed’: No such file or directory mv: cannot stat ‘SRX6619593.20.bb’: No such file or directory