Job ID = 14170569 SRX = SRX9720890 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10741571 spots for SRR13291880/SRR13291880.sra Written 10741571 spots for SRR13291880/SRR13291880.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170979 ("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: 00:03:43 10741571 reads; of these: 10741571 (100.00%) were unpaired; of these: 532785 (4.96%) aligned 0 times 6710089 (62.47%) aligned exactly 1 time 3498697 (32.57%) aligned >1 times 95.04% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 898891 / 10208786 = 0.0881 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.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, 11 Dec 2021 07:24:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:24:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:24:09: 1000000 INFO @ Sat, 11 Dec 2021 07:24:14: 2000000 INFO @ Sat, 11 Dec 2021 07:24:19: 3000000 INFO @ Sat, 11 Dec 2021 07:24:24: 4000000 INFO @ Sat, 11 Dec 2021 07:24:29: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:24:33: 6000000 INFO @ Sat, 11 Dec 2021 07:24:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.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, 11 Dec 2021 07:24:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:24:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:24:38: 7000000 INFO @ Sat, 11 Dec 2021 07:24:39: 1000000 INFO @ Sat, 11 Dec 2021 07:24:43: 8000000 INFO @ Sat, 11 Dec 2021 07:24:44: 2000000 INFO @ Sat, 11 Dec 2021 07:24:48: 9000000 INFO @ Sat, 11 Dec 2021 07:24:49: 3000000 INFO @ Sat, 11 Dec 2021 07:24:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:24:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:24:50: #1 total tags in treatment: 9309895 INFO @ Sat, 11 Dec 2021 07:24:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:24:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:24:50: #1 tags after filtering in treatment: 9309895 INFO @ Sat, 11 Dec 2021 07:24:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:24:50: #1 finished! INFO @ Sat, 11 Dec 2021 07:24:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:24:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:24:50: #2 number of paired peaks: 619 WARNING @ Sat, 11 Dec 2021 07:24:50: Fewer paired peaks (619) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 619 pairs to build model! INFO @ Sat, 11 Dec 2021 07:24:50: start model_add_line... INFO @ Sat, 11 Dec 2021 07:24:50: start X-correlation... INFO @ Sat, 11 Dec 2021 07:24:50: end of X-cor INFO @ Sat, 11 Dec 2021 07:24:50: #2 finished! INFO @ Sat, 11 Dec 2021 07:24:50: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:24:50: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 07:24:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.05_model.r WARNING @ Sat, 11 Dec 2021 07:24:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:24:50: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 07:24:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:24:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:24:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:24:54: 4000000 INFO @ Sat, 11 Dec 2021 07:24:58: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:25:03: 6000000 INFO @ Sat, 11 Dec 2021 07:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.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, 11 Dec 2021 07:25:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:25:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:25:08: 7000000 INFO @ Sat, 11 Dec 2021 07:25:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:25:10: 1000000 INFO @ Sat, 11 Dec 2021 07:25:13: 8000000 INFO @ Sat, 11 Dec 2021 07:25:16: 2000000 INFO @ Sat, 11 Dec 2021 07:25:18: 9000000 INFO @ Sat, 11 Dec 2021 07:25:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:25:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:25:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.05_summits.bed INFO @ Sat, 11 Dec 2021 07:25:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2717 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:25:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:25:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:25:19: #1 total tags in treatment: 9309895 INFO @ Sat, 11 Dec 2021 07:25:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:25:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:25:19: #1 tags after filtering in treatment: 9309895 INFO @ Sat, 11 Dec 2021 07:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:25:19: #1 finished! INFO @ Sat, 11 Dec 2021 07:25:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:25:20: #2 number of paired peaks: 619 WARNING @ Sat, 11 Dec 2021 07:25:20: Fewer paired peaks (619) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 619 pairs to build model! INFO @ Sat, 11 Dec 2021 07:25:20: start model_add_line... INFO @ Sat, 11 Dec 2021 07:25:20: start X-correlation... INFO @ Sat, 11 Dec 2021 07:25:20: end of X-cor INFO @ Sat, 11 Dec 2021 07:25:20: #2 finished! INFO @ Sat, 11 Dec 2021 07:25:20: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:25:20: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 07:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.10_model.r WARNING @ Sat, 11 Dec 2021 07:25:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:25:20: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 07:25:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:25:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:25:21: 3000000 INFO @ Sat, 11 Dec 2021 07:25:27: 4000000 INFO @ Sat, 11 Dec 2021 07:25:32: 5000000 INFO @ Sat, 11 Dec 2021 07:25:38: 6000000 INFO @ Sat, 11 Dec 2021 07:25:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:25:43: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:25:49: 8000000 INFO @ Sat, 11 Dec 2021 07:25:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:25:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:25:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.10_summits.bed INFO @ Sat, 11 Dec 2021 07:25:49: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1554 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:25:55: 9000000 INFO @ Sat, 11 Dec 2021 07:25:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:25:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:25:56: #1 total tags in treatment: 9309895 INFO @ Sat, 11 Dec 2021 07:25:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:25:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:25:56: #1 tags after filtering in treatment: 9309895 INFO @ Sat, 11 Dec 2021 07:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:25:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:25:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:25:57: #2 number of paired peaks: 619 WARNING @ Sat, 11 Dec 2021 07:25:57: Fewer paired peaks (619) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 619 pairs to build model! INFO @ Sat, 11 Dec 2021 07:25:57: start model_add_line... INFO @ Sat, 11 Dec 2021 07:25:57: start X-correlation... INFO @ Sat, 11 Dec 2021 07:25:57: end of X-cor INFO @ Sat, 11 Dec 2021 07:25:57: #2 finished! INFO @ Sat, 11 Dec 2021 07:25:57: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:25:57: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sat, 11 Dec 2021 07:25:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.20_model.r WARNING @ Sat, 11 Dec 2021 07:25:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:25:57: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sat, 11 Dec 2021 07:25:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:25:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:25:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:26:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:26:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:26:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:26:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720890/SRX9720890.20_summits.bed INFO @ Sat, 11 Dec 2021 07:26:26: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (466 records, 4 fields): 2 millis CompletedMACS2peakCalling