Job ID = 6497448 SRX = SRX494946 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:13:15 prefetch.2.10.7: 1) Downloading 'SRR1198478'... 2020-06-25T22:13:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:16:30 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:16:30 prefetch.2.10.7: 1) 'SRR1198478' was downloaded successfully Read 30472199 spots for SRR1198478/SRR1198478.sra Written 30472199 spots for SRR1198478/SRR1198478.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: 00:06:11 30472199 reads; of these: 30472199 (100.00%) were unpaired; of these: 4819578 (15.82%) aligned 0 times 21496221 (70.54%) aligned exactly 1 time 4156400 (13.64%) aligned >1 times 84.18% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 8543988 / 25652621 = 0.3331 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 07:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.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 07:30:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:45: 1000000 INFO @ Fri, 26 Jun 2020 07:30:51: 2000000 INFO @ Fri, 26 Jun 2020 07:30:57: 3000000 INFO @ Fri, 26 Jun 2020 07:31:03: 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 @ Fri, 26 Jun 2020 07:31:10: 5000000 INFO @ Fri, 26 Jun 2020 07:31:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.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 07:31:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:16: 6000000 INFO @ Fri, 26 Jun 2020 07:31:16: 1000000 INFO @ Fri, 26 Jun 2020 07:31:23: 7000000 INFO @ Fri, 26 Jun 2020 07:31:23: 2000000 INFO @ Fri, 26 Jun 2020 07:31:29: 8000000 INFO @ Fri, 26 Jun 2020 07:31:30: 3000000 INFO @ Fri, 26 Jun 2020 07:31:36: 9000000 INFO @ Fri, 26 Jun 2020 07:31:36: 4000000 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 07:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.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 07:31:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:43: 10000000 INFO @ Fri, 26 Jun 2020 07:31:43: 5000000 INFO @ Fri, 26 Jun 2020 07:31:46: 1000000 INFO @ Fri, 26 Jun 2020 07:31:49: 11000000 INFO @ Fri, 26 Jun 2020 07:31:50: 6000000 INFO @ Fri, 26 Jun 2020 07:31:53: 2000000 INFO @ Fri, 26 Jun 2020 07:31:56: 12000000 INFO @ Fri, 26 Jun 2020 07:31:56: 7000000 INFO @ Fri, 26 Jun 2020 07:32:00: 3000000 INFO @ Fri, 26 Jun 2020 07:32:03: 13000000 INFO @ Fri, 26 Jun 2020 07:32:03: 8000000 INFO @ Fri, 26 Jun 2020 07:32:07: 4000000 INFO @ Fri, 26 Jun 2020 07:32:09: 14000000 INFO @ Fri, 26 Jun 2020 07:32:10: 9000000 INFO @ Fri, 26 Jun 2020 07:32:13: 5000000 INFO @ Fri, 26 Jun 2020 07:32:16: 15000000 INFO @ Fri, 26 Jun 2020 07:32:17: 10000000 INFO @ Fri, 26 Jun 2020 07:32:20: 6000000 INFO @ Fri, 26 Jun 2020 07:32:23: 16000000 INFO @ Fri, 26 Jun 2020 07:32:23: 11000000 INFO @ Fri, 26 Jun 2020 07:32:27: 7000000 INFO @ Fri, 26 Jun 2020 07:32:29: 17000000 INFO @ Fri, 26 Jun 2020 07:32:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:32:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:32:30: #1 total tags in treatment: 17108633 INFO @ Fri, 26 Jun 2020 07:32:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:32:30: #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 07:32:30: 12000000 INFO @ Fri, 26 Jun 2020 07:32:30: #1 tags after filtering in treatment: 17108633 INFO @ Fri, 26 Jun 2020 07:32:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:32:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:32:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:32:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:32:32: #2 number of paired peaks: 156 WARNING @ Fri, 26 Jun 2020 07:32:32: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 26 Jun 2020 07:32:32: start model_add_line... INFO @ Fri, 26 Jun 2020 07:32:32: start X-correlation... INFO @ Fri, 26 Jun 2020 07:32:32: end of X-cor INFO @ Fri, 26 Jun 2020 07:32:32: #2 finished! INFO @ Fri, 26 Jun 2020 07:32:32: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:32:32: #2 alternative fragment length(s) may be 1,33,46,363,495,546,564,595 bps INFO @ Fri, 26 Jun 2020 07:32:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.05_model.r WARNING @ Fri, 26 Jun 2020 07:32:32: #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 07:32:32: #2 You may need to consider one of the other alternative d(s): 1,33,46,363,495,546,564,595 WARNING @ Fri, 26 Jun 2020 07:32:32: #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 07:32:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:32:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:32:34: 8000000 INFO @ Fri, 26 Jun 2020 07:32:37: 13000000 INFO @ Fri, 26 Jun 2020 07:32:40: 9000000 INFO @ Fri, 26 Jun 2020 07:32:44: 14000000 INFO @ Fri, 26 Jun 2020 07:32:47: 10000000 INFO @ Fri, 26 Jun 2020 07:32:50: 15000000 INFO @ Fri, 26 Jun 2020 07:32:54: 11000000 INFO @ Fri, 26 Jun 2020 07:32:57: 16000000 INFO @ Fri, 26 Jun 2020 07:33:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:33:01: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:33:04: 17000000 INFO @ Fri, 26 Jun 2020 07:33:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:33:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:33:05: #1 total tags in treatment: 17108633 INFO @ Fri, 26 Jun 2020 07:33:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:05: #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 07:33:05: #1 tags after filtering in treatment: 17108633 INFO @ Fri, 26 Jun 2020 07:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:33:05: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:33:06: #2 number of paired peaks: 156 WARNING @ Fri, 26 Jun 2020 07:33:06: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 26 Jun 2020 07:33:06: start model_add_line... INFO @ Fri, 26 Jun 2020 07:33:06: start X-correlation... INFO @ Fri, 26 Jun 2020 07:33:06: end of X-cor INFO @ Fri, 26 Jun 2020 07:33:06: #2 finished! INFO @ Fri, 26 Jun 2020 07:33:06: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:33:06: #2 alternative fragment length(s) may be 1,33,46,363,495,546,564,595 bps INFO @ Fri, 26 Jun 2020 07:33:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.10_model.r WARNING @ Fri, 26 Jun 2020 07:33:06: #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 07:33:06: #2 You may need to consider one of the other alternative d(s): 1,33,46,363,495,546,564,595 WARNING @ Fri, 26 Jun 2020 07:33:06: #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 07:33:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:33:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:33:07: 13000000 INFO @ Fri, 26 Jun 2020 07:33:14: 14000000 INFO @ Fri, 26 Jun 2020 07:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.05_summits.bed INFO @ Fri, 26 Jun 2020 07:33:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:33:20: 15000000 INFO @ Fri, 26 Jun 2020 07:33:26: 16000000 INFO @ Fri, 26 Jun 2020 07:33:33: 17000000 INFO @ Fri, 26 Jun 2020 07:33:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:33:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:33:33: #1 total tags in treatment: 17108633 INFO @ Fri, 26 Jun 2020 07:33:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:33: #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 07:33:34: #1 tags after filtering in treatment: 17108633 INFO @ Fri, 26 Jun 2020 07:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:33:34: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:33:35: #2 number of paired peaks: 156 WARNING @ Fri, 26 Jun 2020 07:33:35: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Fri, 26 Jun 2020 07:33:35: start model_add_line... INFO @ Fri, 26 Jun 2020 07:33:35: start X-correlation... INFO @ Fri, 26 Jun 2020 07:33:35: end of X-cor INFO @ Fri, 26 Jun 2020 07:33:35: #2 finished! INFO @ Fri, 26 Jun 2020 07:33:35: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:33:35: #2 alternative fragment length(s) may be 1,33,46,363,495,546,564,595 bps INFO @ Fri, 26 Jun 2020 07:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.20_model.r INFO @ Fri, 26 Jun 2020 07:33:35: #3 Call peaks for each chromosome... WARNING @ Fri, 26 Jun 2020 07:33:40: #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 07:33:40: #2 You may need to consider one of the other alternative d(s): 1,33,46,363,495,546,564,595 WARNING @ Fri, 26 Jun 2020 07:33:40: #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 07:33:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:33:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:33:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:33:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:33:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.10_summits.bed INFO @ Fri, 26 Jun 2020 07:33:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:34:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494946/SRX494946.20_summits.bed INFO @ Fri, 26 Jun 2020 07:34:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling