Job ID = 6626465 SRX = SRX5734952 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21471874 spots for SRR8955177/SRR8955177.sra Written 21471874 spots for SRR8955177/SRR8955177.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626615 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:46 21471874 reads; of these: 21471874 (100.00%) were unpaired; of these: 2642305 (12.31%) aligned 0 times 16023441 (74.63%) aligned exactly 1 time 2806128 (13.07%) aligned >1 times 87.69% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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] 8951734 / 18829569 = 0.4754 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, 14 Jul 2020 07:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.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 @ Tue, 14 Jul 2020 07:17:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:17:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:17:39: 1000000 INFO @ Tue, 14 Jul 2020 07:17:46: 2000000 INFO @ Tue, 14 Jul 2020 07:17:53: 3000000 INFO @ Tue, 14 Jul 2020 07:18:00: 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, 14 Jul 2020 07:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.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 @ Tue, 14 Jul 2020 07:18:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:18:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:18:07: 5000000 INFO @ Tue, 14 Jul 2020 07:18:10: 1000000 INFO @ Tue, 14 Jul 2020 07:18:15: 6000000 INFO @ Tue, 14 Jul 2020 07:18:17: 2000000 INFO @ Tue, 14 Jul 2020 07:18:22: 7000000 INFO @ Tue, 14 Jul 2020 07:18:24: 3000000 INFO @ Tue, 14 Jul 2020 07:18:29: 8000000 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, 14 Jul 2020 07:18:31: 4000000 INFO @ Tue, 14 Jul 2020 07:18:36: 9000000 INFO @ Tue, 14 Jul 2020 07:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.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 @ Tue, 14 Jul 2020 07:18:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:18:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:18:39: 5000000 INFO @ Tue, 14 Jul 2020 07:18:42: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 07:18:42: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 07:18:42: #1 total tags in treatment: 9877835 INFO @ Tue, 14 Jul 2020 07:18:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:18:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:18:42: #1 tags after filtering in treatment: 9877835 INFO @ Tue, 14 Jul 2020 07:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:18:42: #1 finished! INFO @ Tue, 14 Jul 2020 07:18:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:18:43: #2 number of paired peaks: 4091 INFO @ Tue, 14 Jul 2020 07:18:43: start model_add_line... INFO @ Tue, 14 Jul 2020 07:18:44: start X-correlation... INFO @ Tue, 14 Jul 2020 07:18:44: end of X-cor INFO @ Tue, 14 Jul 2020 07:18:44: #2 finished! INFO @ Tue, 14 Jul 2020 07:18:44: #2 predicted fragment length is 1 bps INFO @ Tue, 14 Jul 2020 07:18:44: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 14 Jul 2020 07:18:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.05_model.r WARNING @ Tue, 14 Jul 2020 07:18:44: #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, 14 Jul 2020 07:18:44: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 14 Jul 2020 07:18:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:18:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:18:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:18:44: 1000000 INFO @ Tue, 14 Jul 2020 07:18:46: 6000000 INFO @ Tue, 14 Jul 2020 07:18:51: 2000000 INFO @ Tue, 14 Jul 2020 07:18:53: 7000000 INFO @ Tue, 14 Jul 2020 07:18:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:18:59: 3000000 INFO @ Tue, 14 Jul 2020 07:19:00: 8000000 INFO @ Tue, 14 Jul 2020 07:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.05_summits.bed INFO @ Tue, 14 Jul 2020 07:19:05: Done! INFO @ Tue, 14 Jul 2020 07:19:06: 4000000 pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:19:07: 9000000 INFO @ Tue, 14 Jul 2020 07:19:13: 5000000 INFO @ Tue, 14 Jul 2020 07:19:14: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 07:19:14: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 07:19:14: #1 total tags in treatment: 9877835 INFO @ Tue, 14 Jul 2020 07:19:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:19:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:19:14: #1 tags after filtering in treatment: 9877835 INFO @ Tue, 14 Jul 2020 07:19:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:19:14: #1 finished! INFO @ Tue, 14 Jul 2020 07:19:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:19:14: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:19:15: #2 number of paired peaks: 4091 INFO @ Tue, 14 Jul 2020 07:19:15: start model_add_line... INFO @ Tue, 14 Jul 2020 07:19:15: start X-correlation... INFO @ Tue, 14 Jul 2020 07:19:15: end of X-cor INFO @ Tue, 14 Jul 2020 07:19:15: #2 finished! INFO @ Tue, 14 Jul 2020 07:19:15: #2 predicted fragment length is 1 bps INFO @ Tue, 14 Jul 2020 07:19:15: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 14 Jul 2020 07:19:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.10_model.r WARNING @ Tue, 14 Jul 2020 07:19:15: #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, 14 Jul 2020 07:19:15: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 14 Jul 2020 07:19:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:19:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:19:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:19:19: 6000000 INFO @ Tue, 14 Jul 2020 07:19:26: 7000000 INFO @ Tue, 14 Jul 2020 07:19:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:19:33: 8000000 INFO @ Tue, 14 Jul 2020 07:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.10_summits.bed INFO @ Tue, 14 Jul 2020 07:19:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:19:39: 9000000 INFO @ Tue, 14 Jul 2020 07:19:45: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 07:19:45: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 07:19:45: #1 total tags in treatment: 9877835 INFO @ Tue, 14 Jul 2020 07:19:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:19:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:19:45: #1 tags after filtering in treatment: 9877835 INFO @ Tue, 14 Jul 2020 07:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:19:45: #1 finished! INFO @ Tue, 14 Jul 2020 07:19:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:19:47: #2 number of paired peaks: 4091 INFO @ Tue, 14 Jul 2020 07:19:47: start model_add_line... INFO @ Tue, 14 Jul 2020 07:19:47: start X-correlation... INFO @ Tue, 14 Jul 2020 07:19:47: end of X-cor INFO @ Tue, 14 Jul 2020 07:19:47: #2 finished! INFO @ Tue, 14 Jul 2020 07:19:47: #2 predicted fragment length is 1 bps INFO @ Tue, 14 Jul 2020 07:19:47: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 14 Jul 2020 07:19:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.20_model.r WARNING @ Tue, 14 Jul 2020 07:19:47: #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, 14 Jul 2020 07:19:47: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 14 Jul 2020 07:19:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:19:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:19:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:20:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5734952/SRX5734952.20_summits.bed INFO @ Tue, 14 Jul 2020 07:20:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling