Job ID = 6367932 SRX = SRX4200541 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:40:17 prefetch.2.10.7: 1) Downloading 'SRR7298007'... 2020-06-15T23:40:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:24 prefetch.2.10.7: 1) 'SRR7298007' was downloaded successfully Read 21509609 spots for SRR7298007/SRR7298007.sra Written 21509609 spots for SRR7298007/SRR7298007.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: 00:03:56 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255418 (1.19%) aligned 0 times 17821471 (82.85%) aligned exactly 1 time 3432720 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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 8 files... [bam_rmdupse_core] 3667642 / 21254191 = 0.1726 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 08:55:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.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 08:55:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:17: 1000000 INFO @ Tue, 16 Jun 2020 08:55:22: 2000000 INFO @ Tue, 16 Jun 2020 08:55:27: 3000000 INFO @ Tue, 16 Jun 2020 08:55:32: 4000000 INFO @ Tue, 16 Jun 2020 08:55:36: 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 08:55:41: 6000000 INFO @ Tue, 16 Jun 2020 08:55:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.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 08:55:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:46: 7000000 INFO @ Tue, 16 Jun 2020 08:55:48: 1000000 INFO @ Tue, 16 Jun 2020 08:55:51: 8000000 INFO @ Tue, 16 Jun 2020 08:55:53: 2000000 INFO @ Tue, 16 Jun 2020 08:55:56: 9000000 INFO @ Tue, 16 Jun 2020 08:55:59: 3000000 INFO @ Tue, 16 Jun 2020 08:56:00: 10000000 INFO @ Tue, 16 Jun 2020 08:56:04: 4000000 INFO @ Tue, 16 Jun 2020 08:56:05: 11000000 INFO @ Tue, 16 Jun 2020 08:56:09: 5000000 INFO @ Tue, 16 Jun 2020 08:56:10: 12000000 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 08:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.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 08:56:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:14: 6000000 INFO @ Tue, 16 Jun 2020 08:56:15: 13000000 INFO @ Tue, 16 Jun 2020 08:56:18: 1000000 INFO @ Tue, 16 Jun 2020 08:56:20: 7000000 INFO @ Tue, 16 Jun 2020 08:56:20: 14000000 INFO @ Tue, 16 Jun 2020 08:56:23: 2000000 INFO @ Tue, 16 Jun 2020 08:56:24: 15000000 INFO @ Tue, 16 Jun 2020 08:56:25: 8000000 INFO @ Tue, 16 Jun 2020 08:56:27: 3000000 INFO @ Tue, 16 Jun 2020 08:56:29: 16000000 INFO @ Tue, 16 Jun 2020 08:56:30: 9000000 INFO @ Tue, 16 Jun 2020 08:56:32: 4000000 INFO @ Tue, 16 Jun 2020 08:56:34: 17000000 INFO @ Tue, 16 Jun 2020 08:56:36: 10000000 INFO @ Tue, 16 Jun 2020 08:56:37: 5000000 INFO @ Tue, 16 Jun 2020 08:56:37: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:56:37: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:56:37: #1 total tags in treatment: 17586549 INFO @ Tue, 16 Jun 2020 08:56:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:37: #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 08:56:37: #1 tags after filtering in treatment: 17586549 INFO @ Tue, 16 Jun 2020 08:56:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:38: #2 number of paired peaks: 213 WARNING @ Tue, 16 Jun 2020 08:56:38: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:39: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:56:39: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 08:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.05_model.r WARNING @ Tue, 16 Jun 2020 08:56:39: #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 08:56:39: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 08:56:39: #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 08:56:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:41: 11000000 INFO @ Tue, 16 Jun 2020 08:56:42: 6000000 INFO @ Tue, 16 Jun 2020 08:56:46: 12000000 INFO @ Tue, 16 Jun 2020 08:56:46: 7000000 INFO @ Tue, 16 Jun 2020 08:56:51: 8000000 INFO @ Tue, 16 Jun 2020 08:56:52: 13000000 INFO @ Tue, 16 Jun 2020 08:56:56: 9000000 INFO @ Tue, 16 Jun 2020 08:56:57: 14000000 INFO @ Tue, 16 Jun 2020 08:57:01: 10000000 INFO @ Tue, 16 Jun 2020 08:57:02: 15000000 INFO @ Tue, 16 Jun 2020 08:57:06: 11000000 INFO @ Tue, 16 Jun 2020 08:57:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:08: 16000000 INFO @ Tue, 16 Jun 2020 08:57:11: 12000000 INFO @ Tue, 16 Jun 2020 08:57:13: 17000000 INFO @ Tue, 16 Jun 2020 08:57:15: 13000000 INFO @ Tue, 16 Jun 2020 08:57:16: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:57:16: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:57:16: #1 total tags in treatment: 17586549 INFO @ Tue, 16 Jun 2020 08:57:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:16: #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 08:57:16: #1 tags after filtering in treatment: 17586549 INFO @ Tue, 16 Jun 2020 08:57:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:17: #2 number of paired peaks: 213 WARNING @ Tue, 16 Jun 2020 08:57:17: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:57:17: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 08:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.10_model.r WARNING @ Tue, 16 Jun 2020 08:57:17: #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 08:57:17: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 08:57:17: #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 08:57:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:20: 14000000 INFO @ Tue, 16 Jun 2020 08:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:25: 15000000 INFO @ Tue, 16 Jun 2020 08:57:30: 16000000 INFO @ Tue, 16 Jun 2020 08:57:34: 17000000 INFO @ Tue, 16 Jun 2020 08:57:37: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:57:37: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:57:37: #1 total tags in treatment: 17586549 INFO @ Tue, 16 Jun 2020 08:57:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:37: #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 08:57:37: #1 tags after filtering in treatment: 17586549 INFO @ Tue, 16 Jun 2020 08:57:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:39: #2 number of paired peaks: 213 WARNING @ Tue, 16 Jun 2020 08:57:39: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:39: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:57:39: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 08:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.20_model.r WARNING @ Tue, 16 Jun 2020 08:57:39: #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 08:57:39: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 08:57:39: #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 08:57:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.10_summits.bed INFO @ Tue, 16 Jun 2020 08:57:57: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200541/SRX4200541.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:20: 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。