Job ID = 6507853 SRX = SRX494937 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:47:45 prefetch.2.10.7: 1) Downloading 'SRR1198469'... 2020-06-26T13:47:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:51:02 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:51:02 prefetch.2.10.7: 1) 'SRR1198469' was downloaded successfully Read 27599297 spots for SRR1198469/SRR1198469.sra Written 27599297 spots for SRR1198469/SRR1198469.sra 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: 00:07:14 27599297 reads; of these: 27599297 (100.00%) were unpaired; of these: 1483731 (5.38%) aligned 0 times 21194511 (76.79%) aligned exactly 1 time 4921055 (17.83%) aligned >1 times 94.62% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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 12 files... [bam_rmdupse_core] 7997531 / 26115566 = 0.3062 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 @ Fri, 26 Jun 2020 23:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.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 @ Fri, 26 Jun 2020 23:08:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:08:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:08:57: 1000000 INFO @ Fri, 26 Jun 2020 23:09:04: 2000000 INFO @ Fri, 26 Jun 2020 23:09:12: 3000000 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 @ Fri, 26 Jun 2020 23:09:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.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 @ Fri, 26 Jun 2020 23:09:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:09:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:09:21: 4000000 INFO @ Fri, 26 Jun 2020 23:09:27: 1000000 INFO @ Fri, 26 Jun 2020 23:09:29: 5000000 INFO @ Fri, 26 Jun 2020 23:09:35: 2000000 INFO @ Fri, 26 Jun 2020 23:09:37: 6000000 INFO @ Fri, 26 Jun 2020 23:09:44: 3000000 INFO @ Fri, 26 Jun 2020 23:09:46: 7000000 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 @ Fri, 26 Jun 2020 23:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.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 @ Fri, 26 Jun 2020 23:09:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:09:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:09:52: 4000000 INFO @ Fri, 26 Jun 2020 23:09:54: 8000000 INFO @ Fri, 26 Jun 2020 23:09:57: 1000000 INFO @ Fri, 26 Jun 2020 23:10:00: 5000000 INFO @ Fri, 26 Jun 2020 23:10:04: 9000000 INFO @ Fri, 26 Jun 2020 23:10:05: 2000000 INFO @ Fri, 26 Jun 2020 23:10:08: 6000000 INFO @ Fri, 26 Jun 2020 23:10:13: 3000000 INFO @ Fri, 26 Jun 2020 23:10:13: 10000000 INFO @ Fri, 26 Jun 2020 23:10:16: 7000000 INFO @ Fri, 26 Jun 2020 23:10:20: 4000000 INFO @ Fri, 26 Jun 2020 23:10:23: 11000000 INFO @ Fri, 26 Jun 2020 23:10:24: 8000000 INFO @ Fri, 26 Jun 2020 23:10:27: 5000000 INFO @ Fri, 26 Jun 2020 23:10:34: 12000000 INFO @ Fri, 26 Jun 2020 23:10:36: 6000000 INFO @ Fri, 26 Jun 2020 23:10:37: 9000000 INFO @ Fri, 26 Jun 2020 23:10:44: 7000000 INFO @ Fri, 26 Jun 2020 23:10:44: 13000000 INFO @ Fri, 26 Jun 2020 23:10:46: 10000000 INFO @ Fri, 26 Jun 2020 23:10:52: 14000000 INFO @ Fri, 26 Jun 2020 23:10:53: 8000000 INFO @ Fri, 26 Jun 2020 23:10:55: 11000000 INFO @ Fri, 26 Jun 2020 23:11:01: 9000000 INFO @ Fri, 26 Jun 2020 23:11:02: 15000000 INFO @ Fri, 26 Jun 2020 23:11:04: 12000000 INFO @ Fri, 26 Jun 2020 23:11:09: 10000000 INFO @ Fri, 26 Jun 2020 23:11:10: 16000000 INFO @ Fri, 26 Jun 2020 23:11:14: 13000000 INFO @ Fri, 26 Jun 2020 23:11:17: 11000000 INFO @ Fri, 26 Jun 2020 23:11:20: 17000000 INFO @ Fri, 26 Jun 2020 23:11:22: 14000000 INFO @ Fri, 26 Jun 2020 23:11:25: 12000000 INFO @ Fri, 26 Jun 2020 23:11:30: 18000000 INFO @ Fri, 26 Jun 2020 23:11:31: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:11:31: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:11:31: #1 total tags in treatment: 18118035 INFO @ Fri, 26 Jun 2020 23:11:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:11:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:11:31: #1 tags after filtering in treatment: 18118035 INFO @ Fri, 26 Jun 2020 23:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:11:31: #1 finished! INFO @ Fri, 26 Jun 2020 23:11:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:11:32: 15000000 INFO @ Fri, 26 Jun 2020 23:11:33: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 23:11:33: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 23:11:33: start model_add_line... INFO @ Fri, 26 Jun 2020 23:11:33: start X-correlation... INFO @ Fri, 26 Jun 2020 23:11:33: end of X-cor INFO @ Fri, 26 Jun 2020 23:11:33: #2 finished! INFO @ Fri, 26 Jun 2020 23:11:33: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:11:33: #2 alternative fragment length(s) may be 1,40 bps INFO @ Fri, 26 Jun 2020 23:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.05_model.r INFO @ Fri, 26 Jun 2020 23:11:33: 13000000 WARNING @ Fri, 26 Jun 2020 23:11:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:11:33: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Fri, 26 Jun 2020 23:11:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:11:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:11:41: 14000000 INFO @ Fri, 26 Jun 2020 23:11:42: 16000000 INFO @ Fri, 26 Jun 2020 23:11:48: 15000000 INFO @ Fri, 26 Jun 2020 23:11:50: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:11:55: 16000000 INFO @ Fri, 26 Jun 2020 23:11:58: 18000000 INFO @ Fri, 26 Jun 2020 23:11:59: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:11:59: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:11:59: #1 total tags in treatment: 18118035 INFO @ Fri, 26 Jun 2020 23:11:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:11:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:11:59: #1 tags after filtering in treatment: 18118035 INFO @ Fri, 26 Jun 2020 23:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:11:59: #1 finished! INFO @ Fri, 26 Jun 2020 23:11:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:12:01: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 23:12:01: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 23:12:01: start model_add_line... INFO @ Fri, 26 Jun 2020 23:12:01: start X-correlation... INFO @ Fri, 26 Jun 2020 23:12:01: end of X-cor INFO @ Fri, 26 Jun 2020 23:12:01: #2 finished! INFO @ Fri, 26 Jun 2020 23:12:01: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:12:01: #2 alternative fragment length(s) may be 1,40 bps INFO @ Fri, 26 Jun 2020 23:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.10_model.r WARNING @ Fri, 26 Jun 2020 23:12:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:12:01: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Fri, 26 Jun 2020 23:12:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:12:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:12:02: 17000000 INFO @ Fri, 26 Jun 2020 23:12:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:12:09: 18000000 INFO @ Fri, 26 Jun 2020 23:12:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:12:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:12:10: #1 total tags in treatment: 18118035 INFO @ Fri, 26 Jun 2020 23:12:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:12:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:12:10: #1 tags after filtering in treatment: 18118035 INFO @ Fri, 26 Jun 2020 23:12:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:12:10: #1 finished! INFO @ Fri, 26 Jun 2020 23:12:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:12:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:12:12: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 23:12:12: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 23:12:12: start model_add_line... INFO @ Fri, 26 Jun 2020 23:12:12: start X-correlation... INFO @ Fri, 26 Jun 2020 23:12:12: end of X-cor INFO @ Fri, 26 Jun 2020 23:12:12: #2 finished! INFO @ Fri, 26 Jun 2020 23:12:12: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:12:12: #2 alternative fragment length(s) may be 1,40 bps INFO @ Fri, 26 Jun 2020 23:12:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.20_model.r WARNING @ Fri, 26 Jun 2020 23:12:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:12:12: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Fri, 26 Jun 2020 23:12:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:12:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:12:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:12:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:12:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:12:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.05_summits.bed INFO @ Fri, 26 Jun 2020 23:12:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:12:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:12:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:12:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:12:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:12:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.10_summits.bed INFO @ Fri, 26 Jun 2020 23:12:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494937/SRX494937.20_summits.bed INFO @ Fri, 26 Jun 2020 23:12:54: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling