Job ID = 6498396 SRX = SRX495231 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:49:48 prefetch.2.10.7: 1) Downloading 'SRR1198736'... 2020-06-25T23:49:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:52:46 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:52:47 prefetch.2.10.7: 'SRR1198736' is valid 2020-06-25T23:52:47 prefetch.2.10.7: 1) 'SRR1198736' was downloaded successfully Read 17988834 spots for SRR1198736/SRR1198736.sra Written 17988834 spots for SRR1198736/SRR1198736.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: 00:03:38 17988834 reads; of these: 17988834 (100.00%) were unpaired; of these: 4164067 (23.15%) aligned 0 times 12275914 (68.24%) aligned exactly 1 time 1548853 (8.61%) aligned >1 times 76.85% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 3740440 / 13824767 = 0.2706 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 09:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.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 09:00:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:00:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:00:47: 1000000 INFO @ Fri, 26 Jun 2020 09:00:53: 2000000 INFO @ Fri, 26 Jun 2020 09:00:58: 3000000 INFO @ Fri, 26 Jun 2020 09:01:04: 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 09:01:10: 5000000 INFO @ Fri, 26 Jun 2020 09:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.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 09:01:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:01:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:01:17: 6000000 INFO @ Fri, 26 Jun 2020 09:01:17: 1000000 INFO @ Fri, 26 Jun 2020 09:01:23: 7000000 INFO @ Fri, 26 Jun 2020 09:01:24: 2000000 INFO @ Fri, 26 Jun 2020 09:01:29: 8000000 INFO @ Fri, 26 Jun 2020 09:01:30: 3000000 INFO @ Fri, 26 Jun 2020 09:01:36: 9000000 INFO @ Fri, 26 Jun 2020 09:01:37: 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 09:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.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 09:01:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:01:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:01:42: 10000000 INFO @ Fri, 26 Jun 2020 09:01:43: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:01:43: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:01:43: #1 total tags in treatment: 10084327 INFO @ Fri, 26 Jun 2020 09:01:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:01:43: #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 09:01:43: #1 tags after filtering in treatment: 10084327 INFO @ Fri, 26 Jun 2020 09:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:01:43: #1 finished! INFO @ Fri, 26 Jun 2020 09:01:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:01:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:01:44: 5000000 INFO @ Fri, 26 Jun 2020 09:01:44: #2 number of paired peaks: 1306 INFO @ Fri, 26 Jun 2020 09:01:44: start model_add_line... INFO @ Fri, 26 Jun 2020 09:01:44: start X-correlation... INFO @ Fri, 26 Jun 2020 09:01:44: end of X-cor INFO @ Fri, 26 Jun 2020 09:01:44: #2 finished! INFO @ Fri, 26 Jun 2020 09:01:44: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 09:01:44: #2 alternative fragment length(s) may be 3 bps INFO @ Fri, 26 Jun 2020 09:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.05_model.r WARNING @ Fri, 26 Jun 2020 09:01:44: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:01:44: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Fri, 26 Jun 2020 09:01:44: #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 09:01:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:01:47: 1000000 INFO @ Fri, 26 Jun 2020 09:01:50: 6000000 INFO @ Fri, 26 Jun 2020 09:01:54: 2000000 INFO @ Fri, 26 Jun 2020 09:01:57: 7000000 INFO @ Fri, 26 Jun 2020 09:02:00: 3000000 INFO @ Fri, 26 Jun 2020 09:02:03: 8000000 INFO @ Fri, 26 Jun 2020 09:02:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:02:07: 4000000 INFO @ Fri, 26 Jun 2020 09:02:10: 9000000 INFO @ Fri, 26 Jun 2020 09:02:13: 5000000 INFO @ Fri, 26 Jun 2020 09:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.05_summits.bed INFO @ Fri, 26 Jun 2020 09:02:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:02:16: 10000000 INFO @ Fri, 26 Jun 2020 09:02:17: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:02:17: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:02:17: #1 total tags in treatment: 10084327 INFO @ Fri, 26 Jun 2020 09:02:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:02:17: #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 09:02:17: #1 tags after filtering in treatment: 10084327 INFO @ Fri, 26 Jun 2020 09:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:02:17: #1 finished! INFO @ Fri, 26 Jun 2020 09:02:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:02:18: #2 number of paired peaks: 1306 INFO @ Fri, 26 Jun 2020 09:02:18: start model_add_line... INFO @ Fri, 26 Jun 2020 09:02:18: start X-correlation... INFO @ Fri, 26 Jun 2020 09:02:18: end of X-cor INFO @ Fri, 26 Jun 2020 09:02:18: #2 finished! INFO @ Fri, 26 Jun 2020 09:02:18: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 09:02:18: #2 alternative fragment length(s) may be 3 bps INFO @ Fri, 26 Jun 2020 09:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.10_model.r WARNING @ Fri, 26 Jun 2020 09:02:18: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:02:18: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Fri, 26 Jun 2020 09:02:18: #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 09:02:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:02:19: 6000000 INFO @ Fri, 26 Jun 2020 09:02:25: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:02:31: 8000000 INFO @ Fri, 26 Jun 2020 09:02:37: 9000000 INFO @ Fri, 26 Jun 2020 09:02:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:02:43: 10000000 INFO @ Fri, 26 Jun 2020 09:02:43: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:02:43: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:02:43: #1 total tags in treatment: 10084327 INFO @ Fri, 26 Jun 2020 09:02:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:02:43: #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 09:02:43: #1 tags after filtering in treatment: 10084327 INFO @ Fri, 26 Jun 2020 09:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:02:43: #1 finished! INFO @ Fri, 26 Jun 2020 09:02:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:02:44: #2 number of paired peaks: 1306 INFO @ Fri, 26 Jun 2020 09:02:44: start model_add_line... INFO @ Fri, 26 Jun 2020 09:02:44: start X-correlation... INFO @ Fri, 26 Jun 2020 09:02:44: end of X-cor INFO @ Fri, 26 Jun 2020 09:02:44: #2 finished! INFO @ Fri, 26 Jun 2020 09:02:44: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 09:02:44: #2 alternative fragment length(s) may be 3 bps INFO @ Fri, 26 Jun 2020 09:02:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.20_model.r WARNING @ Fri, 26 Jun 2020 09:02:44: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:02:44: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Fri, 26 Jun 2020 09:02:44: #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 09:02:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:02:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.10_summits.bed INFO @ Fri, 26 Jun 2020 09:02:50: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:03:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:03:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:03:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:03:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495231/SRX495231.20_summits.bed INFO @ Fri, 26 Jun 2020 09:03:16: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling