Job ID = 6529438 SRX = SRX2734368 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:12 29987095 reads; of these: 29987095 (100.00%) were unpaired; of these: 1616197 (5.39%) aligned 0 times 24248487 (80.86%) aligned exactly 1 time 4122411 (13.75%) aligned >1 times 94.61% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3901515 / 28370898 = 0.1375 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 @ Tue, 30 Jun 2020 02:16:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.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 @ Tue, 30 Jun 2020 02:16:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:50: 1000000 INFO @ Tue, 30 Jun 2020 02:16:57: 2000000 INFO @ Tue, 30 Jun 2020 02:17:03: 3000000 INFO @ Tue, 30 Jun 2020 02:17:09: 4000000 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 @ Tue, 30 Jun 2020 02:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.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 @ Tue, 30 Jun 2020 02:17:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:15: 5000000 INFO @ Tue, 30 Jun 2020 02:17:20: 1000000 INFO @ Tue, 30 Jun 2020 02:17:22: 6000000 INFO @ Tue, 30 Jun 2020 02:17:25: 2000000 INFO @ Tue, 30 Jun 2020 02:17:28: 7000000 INFO @ Tue, 30 Jun 2020 02:17:31: 3000000 INFO @ Tue, 30 Jun 2020 02:17:34: 8000000 INFO @ Tue, 30 Jun 2020 02:17:37: 4000000 INFO @ Tue, 30 Jun 2020 02:17:41: 9000000 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 @ Tue, 30 Jun 2020 02:17:42: 5000000 INFO @ Tue, 30 Jun 2020 02:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.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 @ Tue, 30 Jun 2020 02:17:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:47: 10000000 INFO @ Tue, 30 Jun 2020 02:17:48: 6000000 INFO @ Tue, 30 Jun 2020 02:17:50: 1000000 INFO @ Tue, 30 Jun 2020 02:17:53: 11000000 INFO @ Tue, 30 Jun 2020 02:17:54: 7000000 INFO @ Tue, 30 Jun 2020 02:17:56: 2000000 INFO @ Tue, 30 Jun 2020 02:17:59: 12000000 INFO @ Tue, 30 Jun 2020 02:18:00: 8000000 INFO @ Tue, 30 Jun 2020 02:18:01: 3000000 INFO @ Tue, 30 Jun 2020 02:18:05: 9000000 INFO @ Tue, 30 Jun 2020 02:18:05: 13000000 INFO @ Tue, 30 Jun 2020 02:18:07: 4000000 INFO @ Tue, 30 Jun 2020 02:18:11: 10000000 INFO @ Tue, 30 Jun 2020 02:18:12: 14000000 INFO @ Tue, 30 Jun 2020 02:18:13: 5000000 INFO @ Tue, 30 Jun 2020 02:18:17: 11000000 INFO @ Tue, 30 Jun 2020 02:18:18: 15000000 INFO @ Tue, 30 Jun 2020 02:18:19: 6000000 INFO @ Tue, 30 Jun 2020 02:18:22: 12000000 INFO @ Tue, 30 Jun 2020 02:18:24: 16000000 INFO @ Tue, 30 Jun 2020 02:18:25: 7000000 INFO @ Tue, 30 Jun 2020 02:18:28: 13000000 INFO @ Tue, 30 Jun 2020 02:18:30: 17000000 INFO @ Tue, 30 Jun 2020 02:18:30: 8000000 INFO @ Tue, 30 Jun 2020 02:18:34: 14000000 INFO @ Tue, 30 Jun 2020 02:18:36: 9000000 INFO @ Tue, 30 Jun 2020 02:18:36: 18000000 INFO @ Tue, 30 Jun 2020 02:18:40: 15000000 INFO @ Tue, 30 Jun 2020 02:18:42: 10000000 INFO @ Tue, 30 Jun 2020 02:18:43: 19000000 INFO @ Tue, 30 Jun 2020 02:18:46: 16000000 INFO @ Tue, 30 Jun 2020 02:18:48: 11000000 INFO @ Tue, 30 Jun 2020 02:18:49: 20000000 INFO @ Tue, 30 Jun 2020 02:18:52: 17000000 INFO @ Tue, 30 Jun 2020 02:18:54: 12000000 INFO @ Tue, 30 Jun 2020 02:18:56: 21000000 INFO @ Tue, 30 Jun 2020 02:18:58: 18000000 INFO @ Tue, 30 Jun 2020 02:19:00: 13000000 INFO @ Tue, 30 Jun 2020 02:19:02: 22000000 INFO @ Tue, 30 Jun 2020 02:19:03: 19000000 INFO @ Tue, 30 Jun 2020 02:19:06: 14000000 INFO @ Tue, 30 Jun 2020 02:19:08: 23000000 INFO @ Tue, 30 Jun 2020 02:19:10: 20000000 INFO @ Tue, 30 Jun 2020 02:19:12: 15000000 INFO @ Tue, 30 Jun 2020 02:19:15: 24000000 INFO @ Tue, 30 Jun 2020 02:19:16: 21000000 INFO @ Tue, 30 Jun 2020 02:19:17: 16000000 INFO @ Tue, 30 Jun 2020 02:19:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:19:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:19:18: #1 total tags in treatment: 24469383 INFO @ Tue, 30 Jun 2020 02:19:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:19:19: #1 tags after filtering in treatment: 24469298 INFO @ Tue, 30 Jun 2020 02:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:21: #2 number of paired peaks: 174 WARNING @ Tue, 30 Jun 2020 02:19:21: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:21: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:19:21: #2 alternative fragment length(s) may be 0,47,109,446,502,533,550,555,570,584 bps INFO @ Tue, 30 Jun 2020 02:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.05_model.r WARNING @ Tue, 30 Jun 2020 02:19:21: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:21: #2 You may need to consider one of the other alternative d(s): 0,47,109,446,502,533,550,555,570,584 WARNING @ Tue, 30 Jun 2020 02:19:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:19:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:21: 22000000 INFO @ Tue, 30 Jun 2020 02:19:23: 17000000 INFO @ Tue, 30 Jun 2020 02:19:27: 23000000 INFO @ Tue, 30 Jun 2020 02:19:29: 18000000 INFO @ Tue, 30 Jun 2020 02:19:33: 24000000 INFO @ Tue, 30 Jun 2020 02:19:35: 19000000 INFO @ Tue, 30 Jun 2020 02:19:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:19:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:19:36: #1 total tags in treatment: 24469383 INFO @ Tue, 30 Jun 2020 02:19:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:19:37: #1 tags after filtering in treatment: 24469298 INFO @ Tue, 30 Jun 2020 02:19:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:38: #2 number of paired peaks: 174 WARNING @ Tue, 30 Jun 2020 02:19:38: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:38: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:38: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:38: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:38: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:38: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:19:38: #2 alternative fragment length(s) may be 0,47,109,446,502,533,550,555,570,584 bps INFO @ Tue, 30 Jun 2020 02:19:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.10_model.r WARNING @ Tue, 30 Jun 2020 02:19:38: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:38: #2 You may need to consider one of the other alternative d(s): 0,47,109,446,502,533,550,555,570,584 WARNING @ Tue, 30 Jun 2020 02:19:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:19:38: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:41: 20000000 INFO @ Tue, 30 Jun 2020 02:19:47: 21000000 INFO @ Tue, 30 Jun 2020 02:19:52: 22000000 INFO @ Tue, 30 Jun 2020 02:19:58: 23000000 INFO @ Tue, 30 Jun 2020 02:20:03: 24000000 INFO @ Tue, 30 Jun 2020 02:20:07: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:20:07: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:20:07: #1 total tags in treatment: 24469383 INFO @ Tue, 30 Jun 2020 02:20:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:20:07: #1 tags after filtering in treatment: 24469298 INFO @ Tue, 30 Jun 2020 02:20:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:09: #2 number of paired peaks: 174 WARNING @ Tue, 30 Jun 2020 02:20:09: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:09: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:09: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:09: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:09: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:09: #2 predicted fragment length is 0 bps INFO @ Tue, 30 Jun 2020 02:20:09: #2 alternative fragment length(s) may be 0,47,109,446,502,533,550,555,570,584 bps INFO @ Tue, 30 Jun 2020 02:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2734368/SRX2734368.20_model.r WARNING @ Tue, 30 Jun 2020 02:20:09: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:09: #2 You may need to consider one of the other alternative d(s): 0,47,109,446,502,533,550,555,570,584 WARNING @ Tue, 30 Jun 2020 02:20:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:20:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at157/job_scripts/6529438: line 293: 38275 Terminated MACS $i /var/spool/uge/at157/job_scripts/6529438: line 293: 59173 Terminated MACS $i /var/spool/uge/at157/job_scripts/6529438: line 293: 77206 Terminated MACS $i ls: cannot access SRX2734368.05.bed: No such file or directory mv: cannot stat ‘SRX2734368.05.bed’: No such file or directory mv: cannot stat ‘SRX2734368.05.bb’: No such file or directory ls: cannot access SRX2734368.10.bed: No such file or directory mv: cannot stat ‘SRX2734368.10.bed’: No such file or directory mv: cannot stat ‘SRX2734368.10.bb’: No such file or directory ls: cannot access SRX2734368.20.bed: No such file or directory mv: cannot stat ‘SRX2734368.20.bed’: No such file or directory mv: cannot stat ‘SRX2734368.20.bb’: No such file or directory