Job ID = 6368194 SRX = SRX494878 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:05:46 prefetch.2.10.7: 1) Downloading 'SRR1198410'... 2020-06-16T00:05:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:11:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:11:16 prefetch.2.10.7: 1) 'SRR1198410' was downloaded successfully Read 32570721 spots for SRR1198410/SRR1198410.sra Written 32570721 spots for SRR1198410/SRR1198410.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: 00:07:50 32570721 reads; of these: 32570721 (100.00%) were unpaired; of these: 778981 (2.39%) aligned 0 times 25992499 (79.80%) aligned exactly 1 time 5799241 (17.81%) aligned >1 times 97.61% overall alignment rate Time searching: 00:07:50 Overall time: 00:07:50 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 16 files... [bam_rmdupse_core] 5125575 / 31791740 = 0.1612 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, 16 Jun 2020 09:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.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 @ Tue, 16 Jun 2020 09:28:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:41: 1000000 INFO @ Tue, 16 Jun 2020 09:28:46: 2000000 INFO @ Tue, 16 Jun 2020 09:28:52: 3000000 INFO @ Tue, 16 Jun 2020 09:28:57: 4000000 INFO @ Tue, 16 Jun 2020 09:29:02: 5000000 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, 16 Jun 2020 09:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.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 @ Tue, 16 Jun 2020 09:29:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:07: 6000000 INFO @ Tue, 16 Jun 2020 09:29:11: 1000000 INFO @ Tue, 16 Jun 2020 09:29:12: 7000000 INFO @ Tue, 16 Jun 2020 09:29:16: 2000000 INFO @ Tue, 16 Jun 2020 09:29:17: 8000000 INFO @ Tue, 16 Jun 2020 09:29:21: 3000000 INFO @ Tue, 16 Jun 2020 09:29:22: 9000000 INFO @ Tue, 16 Jun 2020 09:29:26: 4000000 INFO @ Tue, 16 Jun 2020 09:29:27: 10000000 INFO @ Tue, 16 Jun 2020 09:29:31: 5000000 INFO @ Tue, 16 Jun 2020 09:29:33: 11000000 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, 16 Jun 2020 09:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.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 @ Tue, 16 Jun 2020 09:29:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:36: 6000000 INFO @ Tue, 16 Jun 2020 09:29:38: 12000000 INFO @ Tue, 16 Jun 2020 09:29:40: 1000000 INFO @ Tue, 16 Jun 2020 09:29:41: 7000000 INFO @ Tue, 16 Jun 2020 09:29:43: 13000000 INFO @ Tue, 16 Jun 2020 09:29:45: 2000000 INFO @ Tue, 16 Jun 2020 09:29:46: 8000000 INFO @ Tue, 16 Jun 2020 09:29:48: 14000000 INFO @ Tue, 16 Jun 2020 09:29:50: 3000000 INFO @ Tue, 16 Jun 2020 09:29:51: 9000000 INFO @ Tue, 16 Jun 2020 09:29:53: 15000000 INFO @ Tue, 16 Jun 2020 09:29:55: 4000000 INFO @ Tue, 16 Jun 2020 09:29:56: 10000000 INFO @ Tue, 16 Jun 2020 09:29:58: 16000000 INFO @ Tue, 16 Jun 2020 09:30:00: 5000000 INFO @ Tue, 16 Jun 2020 09:30:01: 11000000 INFO @ Tue, 16 Jun 2020 09:30:03: 17000000 INFO @ Tue, 16 Jun 2020 09:30:05: 6000000 INFO @ Tue, 16 Jun 2020 09:30:06: 12000000 INFO @ Tue, 16 Jun 2020 09:30:07: 18000000 INFO @ Tue, 16 Jun 2020 09:30:10: 7000000 INFO @ Tue, 16 Jun 2020 09:30:11: 13000000 INFO @ Tue, 16 Jun 2020 09:30:12: 19000000 INFO @ Tue, 16 Jun 2020 09:30:15: 8000000 INFO @ Tue, 16 Jun 2020 09:30:16: 14000000 INFO @ Tue, 16 Jun 2020 09:30:17: 20000000 INFO @ Tue, 16 Jun 2020 09:30:20: 9000000 INFO @ Tue, 16 Jun 2020 09:30:21: 15000000 INFO @ Tue, 16 Jun 2020 09:30:22: 21000000 INFO @ Tue, 16 Jun 2020 09:30:24: 10000000 INFO @ Tue, 16 Jun 2020 09:30:26: 16000000 INFO @ Tue, 16 Jun 2020 09:30:27: 22000000 INFO @ Tue, 16 Jun 2020 09:30:29: 11000000 INFO @ Tue, 16 Jun 2020 09:30:31: 17000000 INFO @ Tue, 16 Jun 2020 09:30:32: 23000000 INFO @ Tue, 16 Jun 2020 09:30:34: 12000000 INFO @ Tue, 16 Jun 2020 09:30:35: 18000000 INFO @ Tue, 16 Jun 2020 09:30:37: 24000000 INFO @ Tue, 16 Jun 2020 09:30:39: 13000000 INFO @ Tue, 16 Jun 2020 09:30:40: 19000000 INFO @ Tue, 16 Jun 2020 09:30:41: 25000000 INFO @ Tue, 16 Jun 2020 09:30:44: 14000000 INFO @ Tue, 16 Jun 2020 09:30:45: 20000000 INFO @ Tue, 16 Jun 2020 09:30:46: 26000000 INFO @ Tue, 16 Jun 2020 09:30:49: 15000000 INFO @ Tue, 16 Jun 2020 09:30:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:50: #1 total tags in treatment: 26666165 INFO @ Tue, 16 Jun 2020 09:30:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:30:50: 21000000 INFO @ Tue, 16 Jun 2020 09:30:50: #1 tags after filtering in treatment: 26666165 INFO @ Tue, 16 Jun 2020 09:30:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:52: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 09:30:52: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:52: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:30:52: #2 alternative fragment length(s) may be 1,41,527,582 bps INFO @ Tue, 16 Jun 2020 09:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.05_model.r WARNING @ Tue, 16 Jun 2020 09:30:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:52: #2 You may need to consider one of the other alternative d(s): 1,41,527,582 WARNING @ Tue, 16 Jun 2020 09:30:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:30:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:53: 16000000 INFO @ Tue, 16 Jun 2020 09:30:55: 22000000 INFO @ Tue, 16 Jun 2020 09:30:58: 17000000 INFO @ Tue, 16 Jun 2020 09:31:00: 23000000 INFO @ Tue, 16 Jun 2020 09:31:03: 18000000 INFO @ Tue, 16 Jun 2020 09:31:05: 24000000 INFO @ Tue, 16 Jun 2020 09:31:08: 19000000 INFO @ Tue, 16 Jun 2020 09:31:09: 25000000 INFO @ Tue, 16 Jun 2020 09:31:13: 20000000 INFO @ Tue, 16 Jun 2020 09:31:14: 26000000 INFO @ Tue, 16 Jun 2020 09:31:18: 21000000 INFO @ Tue, 16 Jun 2020 09:31:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:18: #1 total tags in treatment: 26666165 INFO @ Tue, 16 Jun 2020 09:31:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:31:18: #1 tags after filtering in treatment: 26666165 INFO @ Tue, 16 Jun 2020 09:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:20: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 09:31:20: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:31:20: #2 alternative fragment length(s) may be 1,41,527,582 bps INFO @ Tue, 16 Jun 2020 09:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:20: #2 You may need to consider one of the other alternative d(s): 1,41,527,582 WARNING @ Tue, 16 Jun 2020 09:31:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:31:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:22: 22000000 INFO @ Tue, 16 Jun 2020 09:31:27: 23000000 INFO @ Tue, 16 Jun 2020 09:31:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:32: 24000000 INFO @ Tue, 16 Jun 2020 09:31:37: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:31:41: 26000000 INFO @ Tue, 16 Jun 2020 09:31:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:45: #1 total tags in treatment: 26666165 INFO @ Tue, 16 Jun 2020 09:31:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:31:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:45: #1 tags after filtering in treatment: 26666165 INFO @ Tue, 16 Jun 2020 09:31:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:47: #2 number of paired peaks: 138 WARNING @ Tue, 16 Jun 2020 09:31:47: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:47: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:31:47: #2 alternative fragment length(s) may be 1,41,527,582 bps INFO @ Tue, 16 Jun 2020 09:31:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.20_model.r WARNING @ Tue, 16 Jun 2020 09:31:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:47: #2 You may need to consider one of the other alternative d(s): 1,41,527,582 WARNING @ Tue, 16 Jun 2020 09:31:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:31:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494878/SRX494878.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:40: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling