Job ID = 14168177 SRX = SRX8723984 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15427364 spots for SRR12213366/SRR12213366.sra Written 15427364 spots for SRR12213366/SRR12213366.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168987 ("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: 00:04:16 15427364 reads; of these: 15427364 (100.00%) were unpaired; of these: 2000155 (12.96%) aligned 0 times 10014540 (64.91%) aligned exactly 1 time 3412669 (22.12%) aligned >1 times 87.04% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 4650146 / 13427209 = 0.3463 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 @ Fri, 10 Dec 2021 16:01:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.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 @ Fri, 10 Dec 2021 16:01:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:01:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:01:15: 1000000 INFO @ Fri, 10 Dec 2021 16:01:20: 2000000 INFO @ Fri, 10 Dec 2021 16:01:25: 3000000 INFO @ Fri, 10 Dec 2021 16:01:30: 4000000 INFO @ Fri, 10 Dec 2021 16:01:36: 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 @ Fri, 10 Dec 2021 16:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.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 @ Fri, 10 Dec 2021 16:01:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:01:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:01:41: 6000000 INFO @ Fri, 10 Dec 2021 16:01:47: 1000000 INFO @ Fri, 10 Dec 2021 16:01:47: 7000000 INFO @ Fri, 10 Dec 2021 16:01:53: 8000000 INFO @ Fri, 10 Dec 2021 16:01:53: 2000000 INFO @ Fri, 10 Dec 2021 16:01:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:01:57: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:01:57: #1 total tags in treatment: 8777063 INFO @ Fri, 10 Dec 2021 16:01:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:01:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:01:58: #1 tags after filtering in treatment: 8777063 INFO @ Fri, 10 Dec 2021 16:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:01:58: #1 finished! INFO @ Fri, 10 Dec 2021 16:01:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:01:58: #2 number of paired peaks: 411 WARNING @ Fri, 10 Dec 2021 16:01:58: Fewer paired peaks (411) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 411 pairs to build model! INFO @ Fri, 10 Dec 2021 16:01:58: start model_add_line... INFO @ Fri, 10 Dec 2021 16:01:58: start X-correlation... INFO @ Fri, 10 Dec 2021 16:01:58: end of X-cor INFO @ Fri, 10 Dec 2021 16:01:58: #2 finished! INFO @ Fri, 10 Dec 2021 16:01:58: #2 predicted fragment length is 60 bps INFO @ Fri, 10 Dec 2021 16:01:58: #2 alternative fragment length(s) may be 60 bps INFO @ Fri, 10 Dec 2021 16:01:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.05_model.r WARNING @ Fri, 10 Dec 2021 16:01:58: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:01:58: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Fri, 10 Dec 2021 16:01:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:01:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:01:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:02:00: 3000000 INFO @ Fri, 10 Dec 2021 16:02:06: 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 @ Fri, 10 Dec 2021 16:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.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 @ Fri, 10 Dec 2021 16:02:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:02:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:02:12: 5000000 INFO @ Fri, 10 Dec 2021 16:02:16: 1000000 INFO @ Fri, 10 Dec 2021 16:02:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:02:19: 6000000 INFO @ Fri, 10 Dec 2021 16:02:22: 2000000 INFO @ Fri, 10 Dec 2021 16:02:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:02:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:02:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.05_summits.bed INFO @ Fri, 10 Dec 2021 16:02:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2334 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:02:25: 7000000 INFO @ Fri, 10 Dec 2021 16:02:28: 3000000 INFO @ Fri, 10 Dec 2021 16:02:32: 8000000 INFO @ Fri, 10 Dec 2021 16:02:34: 4000000 INFO @ Fri, 10 Dec 2021 16:02:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:02:37: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:02:37: #1 total tags in treatment: 8777063 INFO @ Fri, 10 Dec 2021 16:02:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:02:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:02:37: #1 tags after filtering in treatment: 8777063 INFO @ Fri, 10 Dec 2021 16:02:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:02:37: #1 finished! INFO @ Fri, 10 Dec 2021 16:02:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:02:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:02:38: #2 number of paired peaks: 411 WARNING @ Fri, 10 Dec 2021 16:02:38: Fewer paired peaks (411) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 411 pairs to build model! INFO @ Fri, 10 Dec 2021 16:02:38: start model_add_line... INFO @ Fri, 10 Dec 2021 16:02:38: start X-correlation... INFO @ Fri, 10 Dec 2021 16:02:38: end of X-cor INFO @ Fri, 10 Dec 2021 16:02:38: #2 finished! INFO @ Fri, 10 Dec 2021 16:02:38: #2 predicted fragment length is 60 bps INFO @ Fri, 10 Dec 2021 16:02:38: #2 alternative fragment length(s) may be 60 bps INFO @ Fri, 10 Dec 2021 16:02:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.10_model.r WARNING @ Fri, 10 Dec 2021 16:02:38: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:02:38: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Fri, 10 Dec 2021 16:02:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:02:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:02:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:02:39: 5000000 INFO @ Fri, 10 Dec 2021 16:02:45: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:02:51: 7000000 INFO @ Fri, 10 Dec 2021 16:02:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:02:56: 8000000 INFO @ Fri, 10 Dec 2021 16:03:01: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:03:01: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:03:01: #1 total tags in treatment: 8777063 INFO @ Fri, 10 Dec 2021 16:03:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:03:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:03:01: #1 tags after filtering in treatment: 8777063 INFO @ Fri, 10 Dec 2021 16:03:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:03:01: #1 finished! INFO @ Fri, 10 Dec 2021 16:03:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:03:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:03:02: #2 number of paired peaks: 411 WARNING @ Fri, 10 Dec 2021 16:03:02: Fewer paired peaks (411) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 411 pairs to build model! INFO @ Fri, 10 Dec 2021 16:03:02: start model_add_line... INFO @ Fri, 10 Dec 2021 16:03:02: start X-correlation... INFO @ Fri, 10 Dec 2021 16:03:02: end of X-cor INFO @ Fri, 10 Dec 2021 16:03:02: #2 finished! INFO @ Fri, 10 Dec 2021 16:03:02: #2 predicted fragment length is 60 bps INFO @ Fri, 10 Dec 2021 16:03:02: #2 alternative fragment length(s) may be 60 bps INFO @ Fri, 10 Dec 2021 16:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.20_model.r WARNING @ Fri, 10 Dec 2021 16:03:02: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:03:02: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Fri, 10 Dec 2021 16:03:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:03:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:03:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.10_summits.bed INFO @ Fri, 10 Dec 2021 16:03:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1520 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:03:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8723984/SRX8723984.20_summits.bed INFO @ Fri, 10 Dec 2021 16:03:27: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (907 records, 4 fields): 3 millis CompletedMACS2peakCalling