Job ID = 16437632 SRX = SRX12261324 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27583319 spots for SRR15972580/SRR15972580.sra Written 27583319 spots for SRR15972580/SRR15972580.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438060 ("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: 00:16:27 27583319 reads; of these: 27583319 (100.00%) were unpaired; of these: 1214891 (4.40%) aligned 0 times 17933947 (65.02%) aligned exactly 1 time 8434481 (30.58%) aligned >1 times 95.60% overall alignment rate Time searching: 00:16:27 Overall time: 00:16:27 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 12 files... [bam_rmdupse_core] 13685242 / 26368428 = 0.5190 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:25:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.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 @ Tue, 02 Aug 2022 13:25:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:25:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:25:07: 1000000 INFO @ Tue, 02 Aug 2022 13:25:14: 2000000 INFO @ Tue, 02 Aug 2022 13:25:21: 3000000 INFO @ Tue, 02 Aug 2022 13:25:27: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:25:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.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 @ Tue, 02 Aug 2022 13:25:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:25:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:25:34: 5000000 INFO @ Tue, 02 Aug 2022 13:25:37: 1000000 INFO @ Tue, 02 Aug 2022 13:25:40: 6000000 INFO @ Tue, 02 Aug 2022 13:25:43: 2000000 INFO @ Tue, 02 Aug 2022 13:25:47: 7000000 INFO @ Tue, 02 Aug 2022 13:25:50: 3000000 INFO @ Tue, 02 Aug 2022 13:25:54: 8000000 INFO @ Tue, 02 Aug 2022 13:25:57: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.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 @ Tue, 02 Aug 2022 13:26:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:26:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:26:01: 9000000 INFO @ Tue, 02 Aug 2022 13:26:03: 5000000 INFO @ Tue, 02 Aug 2022 13:26:07: 10000000 INFO @ Tue, 02 Aug 2022 13:26:08: 1000000 INFO @ Tue, 02 Aug 2022 13:26:10: 6000000 INFO @ Tue, 02 Aug 2022 13:26:14: 11000000 INFO @ Tue, 02 Aug 2022 13:26:15: 2000000 INFO @ Tue, 02 Aug 2022 13:26:16: 7000000 INFO @ Tue, 02 Aug 2022 13:26:21: 12000000 INFO @ Tue, 02 Aug 2022 13:26:23: 8000000 INFO @ Tue, 02 Aug 2022 13:26:23: 3000000 INFO @ Tue, 02 Aug 2022 13:26:25: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:26:25: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:26:25: #1 total tags in treatment: 12683186 INFO @ Tue, 02 Aug 2022 13:26:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:26:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:26:26: #1 tags after filtering in treatment: 12683186 INFO @ Tue, 02 Aug 2022 13:26:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:26:26: #1 finished! INFO @ Tue, 02 Aug 2022 13:26:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:26:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:26:27: #2 number of paired peaks: 206 WARNING @ Tue, 02 Aug 2022 13:26:27: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 02 Aug 2022 13:26:27: start model_add_line... INFO @ Tue, 02 Aug 2022 13:26:27: start X-correlation... INFO @ Tue, 02 Aug 2022 13:26:27: end of X-cor INFO @ Tue, 02 Aug 2022 13:26:27: #2 finished! INFO @ Tue, 02 Aug 2022 13:26:27: #2 predicted fragment length is 90 bps INFO @ Tue, 02 Aug 2022 13:26:27: #2 alternative fragment length(s) may be 90 bps INFO @ Tue, 02 Aug 2022 13:26:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.05_model.r WARNING @ Tue, 02 Aug 2022 13:26:27: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:26:27: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Tue, 02 Aug 2022 13:26:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:26:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:26:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:26:30: 9000000 INFO @ Tue, 02 Aug 2022 13:26:31: 4000000 INFO @ Tue, 02 Aug 2022 13:26:37: 10000000 INFO @ Tue, 02 Aug 2022 13:26:39: 5000000 INFO @ Tue, 02 Aug 2022 13:26:43: 11000000 INFO @ Tue, 02 Aug 2022 13:26:47: 6000000 INFO @ Tue, 02 Aug 2022 13:26:50: 12000000 INFO @ Tue, 02 Aug 2022 13:26:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:26:55: 7000000 INFO @ Tue, 02 Aug 2022 13:26:55: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:26:55: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:26:55: #1 total tags in treatment: 12683186 INFO @ Tue, 02 Aug 2022 13:26:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:26:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:26:55: #1 tags after filtering in treatment: 12683186 INFO @ Tue, 02 Aug 2022 13:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:26:55: #1 finished! INFO @ Tue, 02 Aug 2022 13:26:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:26:56: #2 number of paired peaks: 206 WARNING @ Tue, 02 Aug 2022 13:26:56: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 02 Aug 2022 13:26:56: start model_add_line... INFO @ Tue, 02 Aug 2022 13:26:56: start X-correlation... INFO @ Tue, 02 Aug 2022 13:26:56: end of X-cor INFO @ Tue, 02 Aug 2022 13:26:56: #2 finished! INFO @ Tue, 02 Aug 2022 13:26:56: #2 predicted fragment length is 90 bps INFO @ Tue, 02 Aug 2022 13:26:56: #2 alternative fragment length(s) may be 90 bps INFO @ Tue, 02 Aug 2022 13:26:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.10_model.r WARNING @ Tue, 02 Aug 2022 13:26:56: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:26:56: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Tue, 02 Aug 2022 13:26:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:26:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:26:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:27:02: 8000000 INFO @ Tue, 02 Aug 2022 13:27:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:27:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:27:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.05_summits.bed INFO @ Tue, 02 Aug 2022 13:27:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13193 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:27:08: 9000000 INFO @ Tue, 02 Aug 2022 13:27:16: 10000000 INFO @ Tue, 02 Aug 2022 13:27:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:27:23: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:27:30: 12000000 INFO @ Tue, 02 Aug 2022 13:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.10_summits.bed INFO @ Tue, 02 Aug 2022 13:27:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5929 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:27:35: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:27:35: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:27:35: #1 total tags in treatment: 12683186 INFO @ Tue, 02 Aug 2022 13:27:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:27:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:27:35: #1 tags after filtering in treatment: 12683186 INFO @ Tue, 02 Aug 2022 13:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:27:35: #1 finished! INFO @ Tue, 02 Aug 2022 13:27:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:27:36: #2 number of paired peaks: 206 WARNING @ Tue, 02 Aug 2022 13:27:36: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Tue, 02 Aug 2022 13:27:36: start model_add_line... INFO @ Tue, 02 Aug 2022 13:27:36: start X-correlation... INFO @ Tue, 02 Aug 2022 13:27:36: end of X-cor INFO @ Tue, 02 Aug 2022 13:27:36: #2 finished! INFO @ Tue, 02 Aug 2022 13:27:36: #2 predicted fragment length is 90 bps INFO @ Tue, 02 Aug 2022 13:27:36: #2 alternative fragment length(s) may be 90 bps INFO @ Tue, 02 Aug 2022 13:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.20_model.r WARNING @ Tue, 02 Aug 2022 13:27:36: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:27:36: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Tue, 02 Aug 2022 13:27:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:27:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:27:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:28:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:28:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:28:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:28:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261324/SRX12261324.20_summits.bed INFO @ Tue, 02 Aug 2022 13:28:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1579 records, 4 fields): 30 millis CompletedMACS2peakCalling