Job ID = 12265718 SRX = SRX7281030 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20982516 spots for SRR10601378/SRR10601378.sra Written 20982516 spots for SRR10601378/SRR10601378.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265924 ("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: 00:06:55 20982516 reads; of these: 20982516 (100.00%) were unpaired; of these: 7137718 (34.02%) aligned 0 times 10858619 (51.75%) aligned exactly 1 time 2986179 (14.23%) aligned >1 times 65.98% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8144879 / 13844798 = 0.5883 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:30:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.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, 03 Apr 2021 08:30:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:30:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:30:48: 1000000 INFO @ Sat, 03 Apr 2021 08:30:54: 2000000 INFO @ Sat, 03 Apr 2021 08:31:00: 3000000 INFO @ Sat, 03 Apr 2021 08:31:06: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.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, 03 Apr 2021 08:31:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:31:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:31:13: 5000000 INFO @ Sat, 03 Apr 2021 08:31:17: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:31:17: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:31:17: #1 total tags in treatment: 5699919 INFO @ Sat, 03 Apr 2021 08:31:17: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:31:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:31:17: #1 tags after filtering in treatment: 5699919 INFO @ Sat, 03 Apr 2021 08:31:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:31:17: #1 finished! INFO @ Sat, 03 Apr 2021 08:31:17: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:31:18: 1000000 INFO @ Sat, 03 Apr 2021 08:31:18: #2 number of paired peaks: 6460 INFO @ Sat, 03 Apr 2021 08:31:18: start model_add_line... INFO @ Sat, 03 Apr 2021 08:31:18: start X-correlation... INFO @ Sat, 03 Apr 2021 08:31:18: end of X-cor INFO @ Sat, 03 Apr 2021 08:31:18: #2 finished! INFO @ Sat, 03 Apr 2021 08:31:18: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 08:31:18: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 08:31:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.05_model.r WARNING @ Sat, 03 Apr 2021 08:31:18: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:31:18: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 08:31:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:31:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:31:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:31:24: 2000000 INFO @ Sat, 03 Apr 2021 08:31:30: 3000000 INFO @ Sat, 03 Apr 2021 08:31:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:31:37: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:31:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:31:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:31:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.05_summits.bed INFO @ Sat, 03 Apr 2021 08:31:40: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (18001 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.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, 03 Apr 2021 08:31:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:31:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:31:43: 5000000 INFO @ Sat, 03 Apr 2021 08:31:47: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:31:47: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:31:47: #1 total tags in treatment: 5699919 INFO @ Sat, 03 Apr 2021 08:31:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:31:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:31:48: #1 tags after filtering in treatment: 5699919 INFO @ Sat, 03 Apr 2021 08:31:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:31:48: #1 finished! INFO @ Sat, 03 Apr 2021 08:31:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:31:48: #2 number of paired peaks: 6460 INFO @ Sat, 03 Apr 2021 08:31:48: start model_add_line... INFO @ Sat, 03 Apr 2021 08:31:48: start X-correlation... INFO @ Sat, 03 Apr 2021 08:31:48: end of X-cor INFO @ Sat, 03 Apr 2021 08:31:48: #2 finished! INFO @ Sat, 03 Apr 2021 08:31:48: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 08:31:48: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 08:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.10_model.r WARNING @ Sat, 03 Apr 2021 08:31:48: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:31:48: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 08:31:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:31:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:31:50: 1000000 INFO @ Sat, 03 Apr 2021 08:31:58: 2000000 INFO @ Sat, 03 Apr 2021 08:32:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:32:06: 3000000 INFO @ Sat, 03 Apr 2021 08:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.10_summits.bed INFO @ Sat, 03 Apr 2021 08:32:11: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12196 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:32:14: 4000000 INFO @ Sat, 03 Apr 2021 08:32:21: 5000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:32:26: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:32:26: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:32:26: #1 total tags in treatment: 5699919 INFO @ Sat, 03 Apr 2021 08:32:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:32:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:32:27: #1 tags after filtering in treatment: 5699919 INFO @ Sat, 03 Apr 2021 08:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:32:27: #1 finished! INFO @ Sat, 03 Apr 2021 08:32:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:32:27: #2 number of paired peaks: 6460 INFO @ Sat, 03 Apr 2021 08:32:27: start model_add_line... INFO @ Sat, 03 Apr 2021 08:32:27: start X-correlation... INFO @ Sat, 03 Apr 2021 08:32:27: end of X-cor INFO @ Sat, 03 Apr 2021 08:32:27: #2 finished! INFO @ Sat, 03 Apr 2021 08:32:27: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 08:32:27: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 08:32:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.20_model.r WARNING @ Sat, 03 Apr 2021 08:32:27: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:32:27: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 08:32:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:32:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:32:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:32:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281030/SRX7281030.20_summits.bed INFO @ Sat, 03 Apr 2021 08:32:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6404 records, 4 fields): 8 millis CompletedMACS2peakCalling