Job ID = 12264879 SRX = SRX3032278 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19679751 spots for SRR5863968/SRR5863968.sra Written 19679751 spots for SRR5863968/SRR5863968.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265071 ("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: 00:05:01 19679751 reads; of these: 19679751 (100.00%) were unpaired; of these: 3637953 (18.49%) aligned 0 times 12959455 (65.85%) aligned exactly 1 time 3082343 (15.66%) aligned >1 times 81.51% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 7081277 / 16041798 = 0.4414 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:04:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.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 @ Sat, 03 Apr 2021 06:04:17: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:17: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:25: 1000000 INFO @ Sat, 03 Apr 2021 06:04:34: 2000000 INFO @ Sat, 03 Apr 2021 06:04:42: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.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 @ Sat, 03 Apr 2021 06:04:47: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:47: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:51: 4000000 INFO @ Sat, 03 Apr 2021 06:04:56: 1000000 INFO @ Sat, 03 Apr 2021 06:04:59: 5000000 INFO @ Sat, 03 Apr 2021 06:05:06: 2000000 INFO @ Sat, 03 Apr 2021 06:05:08: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:05:15: 3000000 INFO @ Sat, 03 Apr 2021 06:05:16: 7000000 INFO @ Sat, 03 Apr 2021 06:05:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.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 @ Sat, 03 Apr 2021 06:05:17: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:05:17: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:05:25: 4000000 INFO @ Sat, 03 Apr 2021 06:05:25: 8000000 INFO @ Sat, 03 Apr 2021 06:05:28: 1000000 INFO @ Sat, 03 Apr 2021 06:05:34: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:05:34: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:05:34: #1 total tags in treatment: 8960521 INFO @ Sat, 03 Apr 2021 06:05:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:05:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:05:34: #1 tags after filtering in treatment: 8960521 INFO @ Sat, 03 Apr 2021 06:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:05:34: #1 finished! INFO @ Sat, 03 Apr 2021 06:05:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:05:35: 5000000 INFO @ Sat, 03 Apr 2021 06:05:35: #2 number of paired peaks: 3608 INFO @ Sat, 03 Apr 2021 06:05:35: start model_add_line... INFO @ Sat, 03 Apr 2021 06:05:35: start X-correlation... INFO @ Sat, 03 Apr 2021 06:05:35: end of X-cor INFO @ Sat, 03 Apr 2021 06:05:35: #2 finished! INFO @ Sat, 03 Apr 2021 06:05:35: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Apr 2021 06:05:35: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 03 Apr 2021 06:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.05_model.r WARNING @ Sat, 03 Apr 2021 06:05:35: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:05:35: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 03 Apr 2021 06:05:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:05:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:05:38: 2000000 INFO @ Sat, 03 Apr 2021 06:05:45: 6000000 INFO @ Sat, 03 Apr 2021 06:05:48: 3000000 INFO @ Sat, 03 Apr 2021 06:05:55: 7000000 INFO @ Sat, 03 Apr 2021 06:05:59: 4000000 INFO @ Sat, 03 Apr 2021 06:06:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:06:05: 8000000 INFO @ Sat, 03 Apr 2021 06:06:09: 5000000 INFO @ Sat, 03 Apr 2021 06:06:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:06:15: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:06:15: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:06:15: #1 total tags in treatment: 8960521 INFO @ Sat, 03 Apr 2021 06:06:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:06:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:06:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:06:15: #1 tags after filtering in treatment: 8960521 INFO @ Sat, 03 Apr 2021 06:06:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:06:15: #1 finished! INFO @ Sat, 03 Apr 2021 06:06:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:06:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.05_summits.bed INFO @ Sat, 03 Apr 2021 06:06:15: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (18594 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:06:16: #2 number of paired peaks: 3608 INFO @ Sat, 03 Apr 2021 06:06:16: start model_add_line... INFO @ Sat, 03 Apr 2021 06:06:16: start X-correlation... INFO @ Sat, 03 Apr 2021 06:06:16: end of X-cor INFO @ Sat, 03 Apr 2021 06:06:16: #2 finished! INFO @ Sat, 03 Apr 2021 06:06:16: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Apr 2021 06:06:16: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 03 Apr 2021 06:06:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.10_model.r WARNING @ Sat, 03 Apr 2021 06:06:16: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:06:16: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 03 Apr 2021 06:06:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:06:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:06:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:06:18: 6000000 INFO @ Sat, 03 Apr 2021 06:06:27: 7000000 INFO @ Sat, 03 Apr 2021 06:06:36: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:06:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:06:45: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:06:45: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:06:45: #1 total tags in treatment: 8960521 INFO @ Sat, 03 Apr 2021 06:06:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:06:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:06:45: #1 tags after filtering in treatment: 8960521 INFO @ Sat, 03 Apr 2021 06:06:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:06:45: #1 finished! INFO @ Sat, 03 Apr 2021 06:06:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:06:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:06:46: #2 number of paired peaks: 3608 INFO @ Sat, 03 Apr 2021 06:06:46: start model_add_line... INFO @ Sat, 03 Apr 2021 06:06:46: start X-correlation... INFO @ Sat, 03 Apr 2021 06:06:46: end of X-cor INFO @ Sat, 03 Apr 2021 06:06:46: #2 finished! INFO @ Sat, 03 Apr 2021 06:06:46: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Apr 2021 06:06:46: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 03 Apr 2021 06:06:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.20_model.r WARNING @ Sat, 03 Apr 2021 06:06:46: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:06:46: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 03 Apr 2021 06:06:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:06:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:06:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:06:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:06:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:06:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.10_summits.bed INFO @ Sat, 03 Apr 2021 06:06:58: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (11496 records, 4 fields): 39 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:07:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:07:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:07:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:07:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032278/SRX3032278.20_summits.bed INFO @ Sat, 03 Apr 2021 06:07:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4530 records, 4 fields): 7 millis CompletedMACS2peakCalling