Job ID = 14170511 SRX = SRX8689070 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7070424 spots for SRR12174303/SRR12174303.sra Written 7070424 spots for SRR12174303/SRR12174303.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170920 ("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: 00:02:55 7070424 reads; of these: 7070424 (100.00%) were unpaired; of these: 276169 (3.91%) aligned 0 times 4261504 (60.27%) aligned exactly 1 time 2532751 (35.82%) aligned >1 times 96.09% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 1553874 / 6794255 = 0.2287 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 07:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.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 07:06:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:06:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:06:33: 1000000 INFO @ Sat, 11 Dec 2021 07:06:39: 2000000 INFO @ Sat, 11 Dec 2021 07:06:45: 3000000 INFO @ Sat, 11 Dec 2021 07:06:51: 4000000 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 07:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.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 07:06:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:06:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:06:57: 5000000 INFO @ Sat, 11 Dec 2021 07:06:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:06:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:06:59: #1 total tags in treatment: 5240381 INFO @ Sat, 11 Dec 2021 07:06:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:06:59: #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 07:06:59: #1 tags after filtering in treatment: 5240381 INFO @ Sat, 11 Dec 2021 07:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:06:59: #1 finished! INFO @ Sat, 11 Dec 2021 07:06:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:06:59: #2 number of paired peaks: 765 WARNING @ Sat, 11 Dec 2021 07:06:59: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Sat, 11 Dec 2021 07:06:59: start model_add_line... INFO @ Sat, 11 Dec 2021 07:06:59: start X-correlation... INFO @ Sat, 11 Dec 2021 07:06:59: end of X-cor INFO @ Sat, 11 Dec 2021 07:06:59: #2 finished! INFO @ Sat, 11 Dec 2021 07:06:59: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:06:59: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.05_model.r WARNING @ Sat, 11 Dec 2021 07:06:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:06:59: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:06:59: #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 07:06:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:07:03: 1000000 INFO @ Sat, 11 Dec 2021 07:07:09: 2000000 INFO @ Sat, 11 Dec 2021 07:07:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:07:15: 3000000 INFO @ Sat, 11 Dec 2021 07:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.05_summits.bed INFO @ Sat, 11 Dec 2021 07:07:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1859 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:07:21: 4000000 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 07:07:26: 5000000 INFO @ Sat, 11 Dec 2021 07:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.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 07:07:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:07:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:07:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:07:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:07:27: #1 total tags in treatment: 5240381 INFO @ Sat, 11 Dec 2021 07:07:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:07:27: #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 07:07:27: #1 tags after filtering in treatment: 5240381 INFO @ Sat, 11 Dec 2021 07:07:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:07:27: #1 finished! INFO @ Sat, 11 Dec 2021 07:07:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:07:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:07:28: #2 number of paired peaks: 765 WARNING @ Sat, 11 Dec 2021 07:07:28: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Sat, 11 Dec 2021 07:07:28: start model_add_line... INFO @ Sat, 11 Dec 2021 07:07:28: start X-correlation... INFO @ Sat, 11 Dec 2021 07:07:28: end of X-cor INFO @ Sat, 11 Dec 2021 07:07:28: #2 finished! INFO @ Sat, 11 Dec 2021 07:07:28: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:07:28: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.10_model.r WARNING @ Sat, 11 Dec 2021 07:07:28: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:07:28: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:07:28: #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 07:07:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:07:33: 1000000 INFO @ Sat, 11 Dec 2021 07:07:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:07:40: 2000000 INFO @ Sat, 11 Dec 2021 07:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.10_summits.bed INFO @ Sat, 11 Dec 2021 07:07:45: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1589 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:07:46: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:07:53: 4000000 INFO @ Sat, 11 Dec 2021 07:07:59: 5000000 INFO @ Sat, 11 Dec 2021 07:08:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:08:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:08:00: #1 total tags in treatment: 5240381 INFO @ Sat, 11 Dec 2021 07:08:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:08:00: #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 07:08:00: #1 tags after filtering in treatment: 5240381 INFO @ Sat, 11 Dec 2021 07:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:08:00: #1 finished! INFO @ Sat, 11 Dec 2021 07:08:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:08:01: #2 number of paired peaks: 765 WARNING @ Sat, 11 Dec 2021 07:08:01: Fewer paired peaks (765) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 765 pairs to build model! INFO @ Sat, 11 Dec 2021 07:08:01: start model_add_line... INFO @ Sat, 11 Dec 2021 07:08:01: start X-correlation... INFO @ Sat, 11 Dec 2021 07:08:01: end of X-cor INFO @ Sat, 11 Dec 2021 07:08:01: #2 finished! INFO @ Sat, 11 Dec 2021 07:08:01: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:08:01: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:08:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.20_model.r WARNING @ Sat, 11 Dec 2021 07:08:01: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:08:01: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:08:01: #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 07:08:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:08:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:08:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:08:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:08:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:08:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689070/SRX8689070.20_summits.bed INFO @ Sat, 11 Dec 2021 07:08:17: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1220 records, 4 fields): 2 millis CompletedMACS2peakCalling