Job ID = 6366826 SRX = SRX2350725 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:23 prefetch.2.10.7: 1) Downloading 'SRR5024034'... 2020-06-15T23:02:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:49 prefetch.2.10.7: 'SRR5024034' is valid 2020-06-15T23:03:49 prefetch.2.10.7: 1) 'SRR5024034' was downloaded successfully Read 11321125 spots for SRR5024034/SRR5024034.sra Written 11321125 spots for SRR5024034/SRR5024034.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: 00:02:35 11321125 reads; of these: 11321125 (100.00%) were unpaired; of these: 605263 (5.35%) aligned 0 times 7978555 (70.47%) aligned exactly 1 time 2737307 (24.18%) aligned >1 times 94.65% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 1555502 / 10715862 = 0.1452 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 08:09:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.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 08:09:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:56: 1000000 INFO @ Tue, 16 Jun 2020 08:10:02: 2000000 INFO @ Tue, 16 Jun 2020 08:10:07: 3000000 INFO @ Tue, 16 Jun 2020 08:10:13: 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 08:10:19: 5000000 INFO @ Tue, 16 Jun 2020 08:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.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 08:10:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:26: 6000000 INFO @ Tue, 16 Jun 2020 08:10:27: 1000000 INFO @ Tue, 16 Jun 2020 08:10:32: 7000000 INFO @ Tue, 16 Jun 2020 08:10:33: 2000000 INFO @ Tue, 16 Jun 2020 08:10:39: 8000000 INFO @ Tue, 16 Jun 2020 08:10:40: 3000000 INFO @ Tue, 16 Jun 2020 08:10:46: 9000000 INFO @ Tue, 16 Jun 2020 08:10:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:10:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:10:47: #1 total tags in treatment: 9160360 INFO @ Tue, 16 Jun 2020 08:10:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:47: #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 08:10:47: 4000000 INFO @ Tue, 16 Jun 2020 08:10:47: #1 tags after filtering in treatment: 9160360 INFO @ Tue, 16 Jun 2020 08:10:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:47: #2 number of paired peaks: 603 WARNING @ Tue, 16 Jun 2020 08:10:47: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:48: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:10:48: #2 alternative fragment length(s) may be 3,52,569,574,591 bps INFO @ Tue, 16 Jun 2020 08:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.05_model.r WARNING @ Tue, 16 Jun 2020 08:10:48: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:48: #2 You may need to consider one of the other alternative d(s): 3,52,569,574,591 WARNING @ Tue, 16 Jun 2020 08:10:48: #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 08:10:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:48: #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 08:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.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 08:10:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:53: 5000000 INFO @ Tue, 16 Jun 2020 08:10:57: 1000000 INFO @ Tue, 16 Jun 2020 08:11:00: 6000000 INFO @ Tue, 16 Jun 2020 08:11:04: 2000000 INFO @ Tue, 16 Jun 2020 08:11:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:07: 7000000 INFO @ Tue, 16 Jun 2020 08:11:11: 3000000 INFO @ Tue, 16 Jun 2020 08:11:13: 8000000 INFO @ Tue, 16 Jun 2020 08:11:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (733 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:18: 4000000 INFO @ Tue, 16 Jun 2020 08:11:20: 9000000 INFO @ Tue, 16 Jun 2020 08:11:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:21: #1 total tags in treatment: 9160360 INFO @ Tue, 16 Jun 2020 08:11:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:21: #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 08:11:21: #1 tags after filtering in treatment: 9160360 INFO @ Tue, 16 Jun 2020 08:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:22: #2 number of paired peaks: 603 WARNING @ Tue, 16 Jun 2020 08:11:22: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:22: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:11:22: #2 alternative fragment length(s) may be 3,52,569,574,591 bps INFO @ Tue, 16 Jun 2020 08:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.10_model.r WARNING @ Tue, 16 Jun 2020 08:11:22: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:22: #2 You may need to consider one of the other alternative d(s): 3,52,569,574,591 WARNING @ Tue, 16 Jun 2020 08:11:22: #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 08:11:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:24: 5000000 INFO @ Tue, 16 Jun 2020 08:11:30: 6000000 INFO @ Tue, 16 Jun 2020 08:11:36: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:43: 8000000 INFO @ Tue, 16 Jun 2020 08:11:49: 9000000 INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:50: Done! INFO @ Tue, 16 Jun 2020 08:11:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:50: #1 total tags in treatment: 9160360 INFO @ Tue, 16 Jun 2020 08:11:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (481 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:50: #1 tags after filtering in treatment: 9160360 INFO @ Tue, 16 Jun 2020 08:11:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:51: #2 number of paired peaks: 603 WARNING @ Tue, 16 Jun 2020 08:11:51: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:51: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:11:51: #2 alternative fragment length(s) may be 3,52,569,574,591 bps INFO @ Tue, 16 Jun 2020 08:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.20_model.r WARNING @ Tue, 16 Jun 2020 08:11:51: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:51: #2 You may need to consider one of the other alternative d(s): 3,52,569,574,591 WARNING @ Tue, 16 Jun 2020 08:11:51: #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 08:11:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:12:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350725/SRX2350725.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling