Job ID = 6498026 SRX = SRX287899 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:55:13 prefetch.2.10.7: 1) Downloading 'SRR870088'... 2020-06-25T22:55:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:56:06 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:56:07 prefetch.2.10.7: 'SRR870088' is valid 2020-06-25T22:56:07 prefetch.2.10.7: 1) 'SRR870088' was downloaded successfully Read 11858412 spots for SRR870088/SRR870088.sra Written 11858412 spots for SRR870088/SRR870088.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: 00:04:49 11858412 reads; of these: 11858412 (100.00%) were unpaired; of these: 492893 (4.16%) aligned 0 times 8290583 (69.91%) aligned exactly 1 time 3074936 (25.93%) aligned >1 times 95.84% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1010208 / 11365519 = 0.0889 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 08:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:05:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:05:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:05:27: 1000000 INFO @ Fri, 26 Jun 2020 08:05:32: 2000000 INFO @ Fri, 26 Jun 2020 08:05:38: 3000000 INFO @ Fri, 26 Jun 2020 08:05:44: 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 08:05:50: 5000000 INFO @ Fri, 26 Jun 2020 08:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:05:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:05:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:05:56: 6000000 INFO @ Fri, 26 Jun 2020 08:05:56: 1000000 INFO @ Fri, 26 Jun 2020 08:06:02: 7000000 INFO @ Fri, 26 Jun 2020 08:06:02: 2000000 INFO @ Fri, 26 Jun 2020 08:06:08: 8000000 INFO @ Fri, 26 Jun 2020 08:06:09: 3000000 INFO @ Fri, 26 Jun 2020 08:06:14: 9000000 INFO @ Fri, 26 Jun 2020 08:06:15: 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 08:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:06:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:06:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:06:21: 10000000 INFO @ Fri, 26 Jun 2020 08:06:21: 5000000 INFO @ Fri, 26 Jun 2020 08:06:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:06:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:06:23: #1 total tags in treatment: 10355311 INFO @ Fri, 26 Jun 2020 08:06:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:06:23: #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 08:06:23: #1 tags after filtering in treatment: 10355311 INFO @ Fri, 26 Jun 2020 08:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:06:23: #1 finished! INFO @ Fri, 26 Jun 2020 08:06:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:06:24: #2 number of paired peaks: 269 WARNING @ Fri, 26 Jun 2020 08:06:24: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 26 Jun 2020 08:06:24: start model_add_line... INFO @ Fri, 26 Jun 2020 08:06:24: start X-correlation... INFO @ Fri, 26 Jun 2020 08:06:24: end of X-cor INFO @ Fri, 26 Jun 2020 08:06:24: #2 finished! INFO @ Fri, 26 Jun 2020 08:06:24: #2 predicted fragment length is 52 bps INFO @ Fri, 26 Jun 2020 08:06:24: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 26 Jun 2020 08:06:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.05_model.r WARNING @ Fri, 26 Jun 2020 08:06:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:06:24: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 26 Jun 2020 08:06:24: #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 08:06:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:06:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:06:27: 1000000 INFO @ Fri, 26 Jun 2020 08:06:27: 6000000 INFO @ Fri, 26 Jun 2020 08:06:34: 7000000 INFO @ Fri, 26 Jun 2020 08:06:34: 2000000 INFO @ Fri, 26 Jun 2020 08:06:40: 8000000 INFO @ Fri, 26 Jun 2020 08:06:42: 3000000 INFO @ Fri, 26 Jun 2020 08:06:46: 9000000 INFO @ Fri, 26 Jun 2020 08:06:49: 4000000 INFO @ Fri, 26 Jun 2020 08:06:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:06:53: 10000000 INFO @ Fri, 26 Jun 2020 08:06:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:06:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:06:55: #1 total tags in treatment: 10355311 INFO @ Fri, 26 Jun 2020 08:06:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:06:55: #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 08:06:55: #1 tags after filtering in treatment: 10355311 INFO @ Fri, 26 Jun 2020 08:06:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:06:55: #1 finished! INFO @ Fri, 26 Jun 2020 08:06:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:06:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:06:56: #2 number of paired peaks: 269 WARNING @ Fri, 26 Jun 2020 08:06:56: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 26 Jun 2020 08:06:56: start model_add_line... INFO @ Fri, 26 Jun 2020 08:06:56: start X-correlation... INFO @ Fri, 26 Jun 2020 08:06:56: end of X-cor INFO @ Fri, 26 Jun 2020 08:06:56: #2 finished! INFO @ Fri, 26 Jun 2020 08:06:56: #2 predicted fragment length is 52 bps INFO @ Fri, 26 Jun 2020 08:06:56: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 26 Jun 2020 08:06:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.10_model.r WARNING @ Fri, 26 Jun 2020 08:06:56: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:06:56: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 26 Jun 2020 08:06:56: #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 08:06:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:06:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:06:56: 5000000 INFO @ Fri, 26 Jun 2020 08:07:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.05_summits.bed INFO @ Fri, 26 Jun 2020 08:07:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1836 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:07:03: 6000000 INFO @ Fri, 26 Jun 2020 08:07:10: 7000000 INFO @ Fri, 26 Jun 2020 08:07:17: 8000000 INFO @ Fri, 26 Jun 2020 08:07:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:07:24: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:07:30: 10000000 INFO @ Fri, 26 Jun 2020 08:07:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:07:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:07:33: #1 total tags in treatment: 10355311 INFO @ Fri, 26 Jun 2020 08:07:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:07:33: #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 08:07:33: #1 tags after filtering in treatment: 10355311 INFO @ Fri, 26 Jun 2020 08:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:07:33: #1 finished! INFO @ Fri, 26 Jun 2020 08:07:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:07:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:07:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:07:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.10_summits.bed INFO @ Fri, 26 Jun 2020 08:07:33: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1277 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:07:34: #2 number of paired peaks: 269 WARNING @ Fri, 26 Jun 2020 08:07:34: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Fri, 26 Jun 2020 08:07:34: start model_add_line... INFO @ Fri, 26 Jun 2020 08:07:34: start X-correlation... INFO @ Fri, 26 Jun 2020 08:07:34: end of X-cor INFO @ Fri, 26 Jun 2020 08:07:34: #2 finished! INFO @ Fri, 26 Jun 2020 08:07:34: #2 predicted fragment length is 52 bps INFO @ Fri, 26 Jun 2020 08:07:34: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 26 Jun 2020 08:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.20_model.r WARNING @ Fri, 26 Jun 2020 08:07:34: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:07:34: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 26 Jun 2020 08:07:34: #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 08:07:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:07:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:07:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:08:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:08:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:08:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287899/SRX287899.20_summits.bed INFO @ Fri, 26 Jun 2020 08:08:10: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (924 records, 4 fields): 5 millis CompletedMACS2peakCalling