Job ID = 14170494 SRX = SRX8689055 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5268211 spots for SRR12174369/SRR12174369.sra Written 5268211 spots for SRR12174369/SRR12174369.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170895 ("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: 00:01:51 5268211 reads; of these: 5268211 (100.00%) were unpaired; of these: 149492 (2.84%) aligned 0 times 3937911 (74.75%) aligned exactly 1 time 1180808 (22.41%) aligned >1 times 97.16% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 242228 / 5118719 = 0.0473 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 07:01:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.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 07:01:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:17: 1000000 INFO @ Sat, 11 Dec 2021 07:01:24: 2000000 INFO @ Sat, 11 Dec 2021 07:01:31: 3000000 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 07:01:38: 4000000 INFO @ Sat, 11 Dec 2021 07:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.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 07:01:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:44: #1 total tags in treatment: 4876491 INFO @ Sat, 11 Dec 2021 07:01:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:44: #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 07:01:44: #1 tags after filtering in treatment: 4876491 INFO @ Sat, 11 Dec 2021 07:01:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:44: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:01:45: #2 number of paired peaks: 288 WARNING @ Sat, 11 Dec 2021 07:01:45: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:45: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:45: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:45: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:45: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:45: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:01:45: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.05_model.r WARNING @ Sat, 11 Dec 2021 07:01:45: #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 07:01:45: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:01:45: #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 07:01:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:01:48: 1000000 INFO @ Sat, 11 Dec 2021 07:01:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:56: 2000000 INFO @ Sat, 11 Dec 2021 07:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.05_summits.bed INFO @ Sat, 11 Dec 2021 07:02:00: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1050 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:02:04: 3000000 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 07:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.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 07:02:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:02:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:02:12: 4000000 INFO @ Sat, 11 Dec 2021 07:02:19: 1000000 INFO @ Sat, 11 Dec 2021 07:02:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:19: #1 total tags in treatment: 4876491 INFO @ Sat, 11 Dec 2021 07:02:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:19: #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 07:02:20: #1 tags after filtering in treatment: 4876491 INFO @ Sat, 11 Dec 2021 07:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:20: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:20: #2 number of paired peaks: 288 WARNING @ Sat, 11 Dec 2021 07:02:20: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:20: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:20: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:20: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:20: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:20: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:02:20: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:02:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.10_model.r WARNING @ Sat, 11 Dec 2021 07:02:20: #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 07:02:20: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:02:20: #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 07:02:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:26: 2000000 INFO @ Sat, 11 Dec 2021 07:02:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:02:34: 3000000 INFO @ Sat, 11 Dec 2021 07:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.10_summits.bed INFO @ Sat, 11 Dec 2021 07:02:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (828 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:02:42: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:02:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:48: #1 total tags in treatment: 4876491 INFO @ Sat, 11 Dec 2021 07:02:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:48: #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 07:02:49: #1 tags after filtering in treatment: 4876491 INFO @ Sat, 11 Dec 2021 07:02:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:49: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:49: #2 number of paired peaks: 288 WARNING @ Sat, 11 Dec 2021 07:02:49: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:49: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:49: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:49: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:49: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:49: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:02:49: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.20_model.r WARNING @ Sat, 11 Dec 2021 07:02:49: #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 07:02:49: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:02:49: #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 07:02:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:03:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689055/SRX8689055.20_summits.bed INFO @ Sat, 11 Dec 2021 07:03:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 2 millis CompletedMACS2peakCalling