Job ID = 6366849 SRX = SRX2350748 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:13:46 prefetch.2.10.7: 1) Downloading 'SRR5024057'... 2020-06-15T23:13:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:46 prefetch.2.10.7: 'SRR5024057' is valid 2020-06-15T23:14:46 prefetch.2.10.7: 1) 'SRR5024057' was downloaded successfully Read 10173885 spots for SRR5024057/SRR5024057.sra Written 10173885 spots for SRR5024057/SRR5024057.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: 00:02:27 10173885 reads; of these: 10173885 (100.00%) were unpaired; of these: 97302 (0.96%) aligned 0 times 8836919 (86.86%) aligned exactly 1 time 1239664 (12.18%) aligned >1 times 99.04% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 1105163 / 10076583 = 0.1097 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 08:20:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.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 08:20:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:52: 1000000 INFO @ Tue, 16 Jun 2020 08:20:58: 2000000 INFO @ Tue, 16 Jun 2020 08:21:03: 3000000 INFO @ Tue, 16 Jun 2020 08:21:09: 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, 16 Jun 2020 08:21:15: 5000000 INFO @ Tue, 16 Jun 2020 08:21:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.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 08:21:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:21: 6000000 INFO @ Tue, 16 Jun 2020 08:21:22: 1000000 INFO @ Tue, 16 Jun 2020 08:21:27: 7000000 INFO @ Tue, 16 Jun 2020 08:21:28: 2000000 INFO @ Tue, 16 Jun 2020 08:21:33: 8000000 INFO @ Tue, 16 Jun 2020 08:21:34: 3000000 INFO @ Tue, 16 Jun 2020 08:21:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:39: #1 total tags in treatment: 8971420 INFO @ Tue, 16 Jun 2020 08:21:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:39: #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 08:21:39: #1 tags after filtering in treatment: 8971420 INFO @ Tue, 16 Jun 2020 08:21:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:40: 4000000 INFO @ Tue, 16 Jun 2020 08:21:40: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 08:21:40: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:40: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:21:40: #2 alternative fragment length(s) may be 3,50,116,463,502,517,547,560 bps INFO @ Tue, 16 Jun 2020 08:21:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.05_model.r WARNING @ Tue, 16 Jun 2020 08:21:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:40: #2 You may need to consider one of the other alternative d(s): 3,50,116,463,502,517,547,560 WARNING @ Tue, 16 Jun 2020 08:21:40: #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 08:21:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:40: #3 Pre-compute pvalue-qvalue table... 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 08:21:45: 5000000 INFO @ Tue, 16 Jun 2020 08:21:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.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 08:21:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:51: 6000000 INFO @ Tue, 16 Jun 2020 08:21:53: 1000000 INFO @ Tue, 16 Jun 2020 08:21:58: 7000000 INFO @ Tue, 16 Jun 2020 08:22:00: 2000000 INFO @ Tue, 16 Jun 2020 08:22:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:04: 8000000 INFO @ Tue, 16 Jun 2020 08:22:06: 3000000 INFO @ Tue, 16 Jun 2020 08:22:10: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:10: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:10: #1 total tags in treatment: 8971420 INFO @ Tue, 16 Jun 2020 08:22:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:10: #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 08:22:10: #1 tags after filtering in treatment: 8971420 INFO @ Tue, 16 Jun 2020 08:22:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:10: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 08:22:10: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:11: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:22:11: #2 alternative fragment length(s) may be 3,50,116,463,502,517,547,560 bps INFO @ Tue, 16 Jun 2020 08:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.10_model.r WARNING @ Tue, 16 Jun 2020 08:22:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:11: #2 You may need to consider one of the other alternative d(s): 3,50,116,463,502,517,547,560 WARNING @ Tue, 16 Jun 2020 08:22:11: #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 08:22:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.05_summits.bed INFO @ Tue, 16 Jun 2020 08:22:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (537 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:13: 4000000 INFO @ Tue, 16 Jun 2020 08:22:19: 5000000 INFO @ Tue, 16 Jun 2020 08:22:26: 6000000 INFO @ Tue, 16 Jun 2020 08:22:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:32: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:39: 8000000 INFO @ Tue, 16 Jun 2020 08:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:45: #1 total tags in treatment: 8971420 INFO @ Tue, 16 Jun 2020 08:22:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:45: #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 08:22:45: #1 tags after filtering in treatment: 8971420 INFO @ Tue, 16 Jun 2020 08:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:46: #2 number of paired peaks: 169 WARNING @ Tue, 16 Jun 2020 08:22:46: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:46: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:22:46: #2 alternative fragment length(s) may be 3,50,116,463,502,517,547,560 bps INFO @ Tue, 16 Jun 2020 08:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.20_model.r WARNING @ Tue, 16 Jun 2020 08:22:46: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:46: #2 You may need to consider one of the other alternative d(s): 3,50,116,463,502,517,547,560 WARNING @ Tue, 16 Jun 2020 08:22:46: #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 08:22:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350748/SRX2350748.20_summits.bed INFO @ Tue, 16 Jun 2020 08:23:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (73 records, 4 fields): 1 millis CompletedMACS2peakCalling