Job ID = 14170517 SRX = SRX8689075 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8937548 spots for SRR12174308/SRR12174308.sra Written 8937548 spots for SRR12174308/SRR12174308.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170925 ("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: 00:02:48 8937548 reads; of these: 8937548 (100.00%) were unpaired; of these: 463470 (5.19%) aligned 0 times 6126464 (68.55%) aligned exactly 1 time 2347614 (26.27%) aligned >1 times 94.81% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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_rmdupse_core] 407718 / 8474078 = 0.0481 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 07:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.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 07:08:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:08:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:08:18: 1000000 INFO @ Sat, 11 Dec 2021 07:08:23: 2000000 INFO @ Sat, 11 Dec 2021 07:08:28: 3000000 INFO @ Sat, 11 Dec 2021 07:08:33: 4000000 INFO @ Sat, 11 Dec 2021 07:08:39: 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 07:08:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.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 07:08:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:08:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:08:44: 6000000 INFO @ Sat, 11 Dec 2021 07:08:48: 1000000 INFO @ Sat, 11 Dec 2021 07:08:50: 7000000 INFO @ Sat, 11 Dec 2021 07:08:54: 2000000 INFO @ Sat, 11 Dec 2021 07:08:55: 8000000 INFO @ Sat, 11 Dec 2021 07:08:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:08:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:08:56: #1 total tags in treatment: 8066360 INFO @ Sat, 11 Dec 2021 07:08:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:08:56: #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 07:08:56: #1 tags after filtering in treatment: 8066360 INFO @ Sat, 11 Dec 2021 07:08:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:08:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:08:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:08:56: #2 number of paired peaks: 239 WARNING @ Sat, 11 Dec 2021 07:08:56: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sat, 11 Dec 2021 07:08:56: start model_add_line... INFO @ Sat, 11 Dec 2021 07:08:56: start X-correlation... INFO @ Sat, 11 Dec 2021 07:08:57: end of X-cor INFO @ Sat, 11 Dec 2021 07:08:57: #2 finished! INFO @ Sat, 11 Dec 2021 07:08:57: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:08:57: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:08:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.05_model.r WARNING @ Sat, 11 Dec 2021 07:08:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:08:57: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:08:57: #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 07:08:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:08:59: 3000000 INFO @ Sat, 11 Dec 2021 07:09:05: 4000000 INFO @ Sat, 11 Dec 2021 07:09:10: 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 07:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.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 07:09:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:09:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:09:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:09:16: 6000000 INFO @ Sat, 11 Dec 2021 07:09:18: 1000000 INFO @ Sat, 11 Dec 2021 07:09:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:09:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:09:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.05_summits.bed INFO @ Sat, 11 Dec 2021 07:09:21: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1218 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:09:22: 7000000 INFO @ Sat, 11 Dec 2021 07:09:24: 2000000 INFO @ Sat, 11 Dec 2021 07:09:28: 8000000 INFO @ Sat, 11 Dec 2021 07:09:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:09:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:09:28: #1 total tags in treatment: 8066360 INFO @ Sat, 11 Dec 2021 07:09:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:09:28: #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 07:09:28: #1 tags after filtering in treatment: 8066360 INFO @ Sat, 11 Dec 2021 07:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:09:28: #1 finished! INFO @ Sat, 11 Dec 2021 07:09:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:09:29: #2 number of paired peaks: 239 WARNING @ Sat, 11 Dec 2021 07:09:29: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sat, 11 Dec 2021 07:09:29: start model_add_line... INFO @ Sat, 11 Dec 2021 07:09:29: start X-correlation... INFO @ Sat, 11 Dec 2021 07:09:29: end of X-cor INFO @ Sat, 11 Dec 2021 07:09:29: #2 finished! INFO @ Sat, 11 Dec 2021 07:09:29: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:09:29: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.10_model.r WARNING @ Sat, 11 Dec 2021 07:09:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:09:29: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:09:29: #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 07:09:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:09:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:09:30: 3000000 INFO @ Sat, 11 Dec 2021 07:09:35: 4000000 INFO @ Sat, 11 Dec 2021 07:09:41: 5000000 INFO @ Sat, 11 Dec 2021 07:09:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:09:46: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:09:52: 7000000 INFO @ Sat, 11 Dec 2021 07:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.10_summits.bed INFO @ Sat, 11 Dec 2021 07:09:52: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:09:57: 8000000 INFO @ Sat, 11 Dec 2021 07:09:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:09:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:09:58: #1 total tags in treatment: 8066360 INFO @ Sat, 11 Dec 2021 07:09:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:09:58: #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 07:09:58: #1 tags after filtering in treatment: 8066360 INFO @ Sat, 11 Dec 2021 07:09:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:09:58: #1 finished! INFO @ Sat, 11 Dec 2021 07:09:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:09:58: #2 number of paired peaks: 239 WARNING @ Sat, 11 Dec 2021 07:09:58: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Sat, 11 Dec 2021 07:09:58: start model_add_line... INFO @ Sat, 11 Dec 2021 07:09:58: start X-correlation... INFO @ Sat, 11 Dec 2021 07:09:58: end of X-cor INFO @ Sat, 11 Dec 2021 07:09:58: #2 finished! INFO @ Sat, 11 Dec 2021 07:09:58: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:09:58: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.20_model.r WARNING @ Sat, 11 Dec 2021 07:09:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:09:58: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:09:58: #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 07:09:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:09:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:10:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:10:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:10:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:10:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689075/SRX8689075.20_summits.bed INFO @ Sat, 11 Dec 2021 07:10:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (750 records, 4 fields): 2 millis CompletedMACS2peakCalling