Job ID = 6626468 SRX = SRX5734954 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19743692 spots for SRR8955179/SRR8955179.sra Written 19743692 spots for SRR8955179/SRR8955179.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626614 ("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: 00:07:33 19743692 reads; of these: 19743692 (100.00%) were unpaired; of these: 2274497 (11.52%) aligned 0 times 14883910 (75.39%) aligned exactly 1 time 2585285 (13.09%) aligned >1 times 88.48% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 7996064 / 17469195 = 0.4577 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 07:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.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 07:17:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:17:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:17:17: 1000000 INFO @ Tue, 14 Jul 2020 07:17:24: 2000000 INFO @ Tue, 14 Jul 2020 07:17:32: 3000000 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 07:17:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.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 07:17:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:17:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:17:39: 4000000 INFO @ Tue, 14 Jul 2020 07:17:47: 1000000 INFO @ Tue, 14 Jul 2020 07:17:48: 5000000 INFO @ Tue, 14 Jul 2020 07:17:56: 2000000 INFO @ Tue, 14 Jul 2020 07:17:56: 6000000 INFO @ Tue, 14 Jul 2020 07:18:04: 7000000 INFO @ Tue, 14 Jul 2020 07:18:04: 3000000 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 07:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.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 07:18:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:18:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:18:12: 8000000 INFO @ Tue, 14 Jul 2020 07:18:13: 4000000 INFO @ Tue, 14 Jul 2020 07:18:17: 1000000 INFO @ Tue, 14 Jul 2020 07:18:20: 9000000 INFO @ Tue, 14 Jul 2020 07:18:21: 5000000 INFO @ Tue, 14 Jul 2020 07:18:24: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 07:18:24: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 07:18:24: #1 total tags in treatment: 9473131 INFO @ Tue, 14 Jul 2020 07:18:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:18:24: #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 07:18:24: #1 tags after filtering in treatment: 9473131 INFO @ Tue, 14 Jul 2020 07:18:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:18:24: #1 finished! INFO @ Tue, 14 Jul 2020 07:18:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:18:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:18:25: 2000000 INFO @ Tue, 14 Jul 2020 07:18:26: #2 number of paired peaks: 3895 INFO @ Tue, 14 Jul 2020 07:18:26: start model_add_line... INFO @ Tue, 14 Jul 2020 07:18:26: start X-correlation... INFO @ Tue, 14 Jul 2020 07:18:26: end of X-cor INFO @ Tue, 14 Jul 2020 07:18:26: #2 finished! INFO @ Tue, 14 Jul 2020 07:18:26: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 07:18:26: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 14 Jul 2020 07:18:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.05_model.r WARNING @ Tue, 14 Jul 2020 07:18:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:18:26: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 14 Jul 2020 07:18:26: #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 07:18:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:18:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:18:30: 6000000 INFO @ Tue, 14 Jul 2020 07:18:33: 3000000 INFO @ Tue, 14 Jul 2020 07:18:38: 7000000 INFO @ Tue, 14 Jul 2020 07:18:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:18:41: 4000000 INFO @ Tue, 14 Jul 2020 07:18:46: 8000000 INFO @ Tue, 14 Jul 2020 07:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.05_summits.bed INFO @ Tue, 14 Jul 2020 07:18:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:18:49: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:18:55: 9000000 INFO @ Tue, 14 Jul 2020 07:18:57: 6000000 INFO @ Tue, 14 Jul 2020 07:18:59: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 07:18:59: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 07:18:59: #1 total tags in treatment: 9473131 INFO @ Tue, 14 Jul 2020 07:18:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:18:59: #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 07:18:59: #1 tags after filtering in treatment: 9473131 INFO @ Tue, 14 Jul 2020 07:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:18:59: #1 finished! INFO @ Tue, 14 Jul 2020 07:18:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:19:00: #2 number of paired peaks: 3895 INFO @ Tue, 14 Jul 2020 07:19:00: start model_add_line... INFO @ Tue, 14 Jul 2020 07:19:00: start X-correlation... INFO @ Tue, 14 Jul 2020 07:19:00: end of X-cor INFO @ Tue, 14 Jul 2020 07:19:00: #2 finished! INFO @ Tue, 14 Jul 2020 07:19:00: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 07:19:00: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 14 Jul 2020 07:19:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.10_model.r WARNING @ Tue, 14 Jul 2020 07:19:00: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:19:00: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 14 Jul 2020 07:19:00: #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 07:19:00: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:19:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:19:05: 7000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:19:13: 8000000 INFO @ Tue, 14 Jul 2020 07:19:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:19:20: 9000000 INFO @ Tue, 14 Jul 2020 07:19:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:19:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:19:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.10_summits.bed INFO @ Tue, 14 Jul 2020 07:19:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:19:23: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 07:19:23: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 07:19:23: #1 total tags in treatment: 9473131 INFO @ Tue, 14 Jul 2020 07:19:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:19:23: #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 07:19:23: #1 tags after filtering in treatment: 9473131 INFO @ Tue, 14 Jul 2020 07:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:19:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:19:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:19:25: #2 number of paired peaks: 3895 INFO @ Tue, 14 Jul 2020 07:19:25: start model_add_line... INFO @ Tue, 14 Jul 2020 07:19:25: start X-correlation... INFO @ Tue, 14 Jul 2020 07:19:25: end of X-cor INFO @ Tue, 14 Jul 2020 07:19:25: #2 finished! INFO @ Tue, 14 Jul 2020 07:19:25: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 07:19:25: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 14 Jul 2020 07:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.20_model.r WARNING @ Tue, 14 Jul 2020 07:19:25: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:19:25: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 14 Jul 2020 07:19:25: #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 07:19:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:19:39: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5734954/SRX5734954.20_summits.bed INFO @ Tue, 14 Jul 2020 07:19:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling