Job ID = 14170448 SRX = SRX8689026 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6573582 spots for SRR12174331/SRR12174331.sra Written 6573582 spots for SRR12174331/SRR12174331.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170852 ("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: 00:02:47 6573582 reads; of these: 6573582 (100.00%) were unpaired; of these: 172609 (2.63%) aligned 0 times 4270164 (64.96%) aligned exactly 1 time 2130809 (32.41%) aligned >1 times 97.37% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 2668114 / 6400973 = 0.4168 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 06:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.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 06:52:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:52:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:52:49: 1000000 INFO @ Sat, 11 Dec 2021 06:52:55: 2000000 INFO @ Sat, 11 Dec 2021 06:53:01: 3000000 INFO @ Sat, 11 Dec 2021 06:53:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:53:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:53:06: #1 total tags in treatment: 3732859 INFO @ Sat, 11 Dec 2021 06:53:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:53:06: #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 06:53:06: #1 tags after filtering in treatment: 3732859 INFO @ Sat, 11 Dec 2021 06:53:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:53:06: #1 finished! INFO @ Sat, 11 Dec 2021 06:53:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:53:06: #2 number of paired peaks: 770 WARNING @ Sat, 11 Dec 2021 06:53:06: Fewer paired peaks (770) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 770 pairs to build model! INFO @ Sat, 11 Dec 2021 06:53:06: start model_add_line... INFO @ Sat, 11 Dec 2021 06:53:06: start X-correlation... INFO @ Sat, 11 Dec 2021 06:53:06: end of X-cor INFO @ Sat, 11 Dec 2021 06:53:06: #2 finished! INFO @ Sat, 11 Dec 2021 06:53:06: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 06:53:06: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 06:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.05_model.r WARNING @ Sat, 11 Dec 2021 06:53:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:53:06: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 06:53:06: #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 06:53:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:53:06: #3 Pre-compute pvalue-qvalue table... 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 06:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.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 06:53:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:53:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:53:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.05_summits.bed INFO @ Sat, 11 Dec 2021 06:53:19: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1471 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:53:20: 1000000 INFO @ Sat, 11 Dec 2021 06:53:26: 2000000 INFO @ Sat, 11 Dec 2021 06:53:32: 3000000 INFO @ Sat, 11 Dec 2021 06:53:37: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:53:37: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:53:37: #1 total tags in treatment: 3732859 INFO @ Sat, 11 Dec 2021 06:53:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:53:37: #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 06:53:37: #1 tags after filtering in treatment: 3732859 INFO @ Sat, 11 Dec 2021 06:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:53:37: #1 finished! INFO @ Sat, 11 Dec 2021 06:53:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:53:37: #2 number of paired peaks: 770 WARNING @ Sat, 11 Dec 2021 06:53:37: Fewer paired peaks (770) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 770 pairs to build model! INFO @ Sat, 11 Dec 2021 06:53:37: start model_add_line... INFO @ Sat, 11 Dec 2021 06:53:37: start X-correlation... INFO @ Sat, 11 Dec 2021 06:53:37: end of X-cor INFO @ Sat, 11 Dec 2021 06:53:37: #2 finished! INFO @ Sat, 11 Dec 2021 06:53:37: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 06:53:37: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 06:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.10_model.r WARNING @ Sat, 11 Dec 2021 06:53:37: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:53:37: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 06:53:37: #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 06:53:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:53:37: #3 Pre-compute pvalue-qvalue table... 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 06:53:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.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 06:53:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:53:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:53:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:49: 1000000 INFO @ Sat, 11 Dec 2021 06:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.10_summits.bed INFO @ Sat, 11 Dec 2021 06:53:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1251 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:53:56: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:54:02: 3000000 INFO @ Sat, 11 Dec 2021 06:54:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:54:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:54:06: #1 total tags in treatment: 3732859 INFO @ Sat, 11 Dec 2021 06:54:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:54:06: #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 06:54:06: #1 tags after filtering in treatment: 3732859 INFO @ Sat, 11 Dec 2021 06:54:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:54:06: #1 finished! INFO @ Sat, 11 Dec 2021 06:54:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:54:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:54:07: #2 number of paired peaks: 770 WARNING @ Sat, 11 Dec 2021 06:54:07: Fewer paired peaks (770) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 770 pairs to build model! INFO @ Sat, 11 Dec 2021 06:54:07: start model_add_line... INFO @ Sat, 11 Dec 2021 06:54:07: start X-correlation... INFO @ Sat, 11 Dec 2021 06:54:07: end of X-cor INFO @ Sat, 11 Dec 2021 06:54:07: #2 finished! INFO @ Sat, 11 Dec 2021 06:54:07: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 06:54:07: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 06:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.20_model.r WARNING @ Sat, 11 Dec 2021 06:54:07: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:54:07: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 06:54:07: #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 06:54:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:54:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:54:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:54:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:54:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:54:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689026/SRX8689026.20_summits.bed INFO @ Sat, 11 Dec 2021 06:54:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (955 records, 4 fields): 3 millis CompletedMACS2peakCalling