Job ID = 12264886 SRX = SRX3032284 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14977357 spots for SRR5863974/SRR5863974.sra Written 14977357 spots for SRR5863974/SRR5863974.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265055 ("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: 00:03:58 14977357 reads; of these: 14977357 (100.00%) were unpaired; of these: 2702200 (18.04%) aligned 0 times 9912002 (66.18%) aligned exactly 1 time 2363155 (15.78%) aligned >1 times 81.96% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 4926407 / 12275157 = 0.4013 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 06:02:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.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 06:02:28: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:28: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:36: 1000000 INFO @ Sat, 03 Apr 2021 06:02:44: 2000000 INFO @ Sat, 03 Apr 2021 06:02:51: 3000000 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 06:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.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 06:02:58: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:58: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:58: 4000000 INFO @ Sat, 03 Apr 2021 06:03:06: 5000000 INFO @ Sat, 03 Apr 2021 06:03:08: 1000000 INFO @ Sat, 03 Apr 2021 06:03:13: 6000000 INFO @ Sat, 03 Apr 2021 06:03:18: 2000000 INFO @ Sat, 03 Apr 2021 06:03:21: 7000000 INFO @ Sat, 03 Apr 2021 06:03:23: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:03:23: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:03:23: #1 total tags in treatment: 7348750 INFO @ Sat, 03 Apr 2021 06:03:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:23: #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 06:03:23: #1 tags after filtering in treatment: 7348750 INFO @ Sat, 03 Apr 2021 06:03:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:23: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:24: #2 number of paired peaks: 4043 INFO @ Sat, 03 Apr 2021 06:03:24: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:24: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:24: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:24: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:24: #2 predicted fragment length is 81 bps INFO @ Sat, 03 Apr 2021 06:03:24: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 03 Apr 2021 06:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.05_model.r WARNING @ Sat, 03 Apr 2021 06:03:24: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:03:24: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 03 Apr 2021 06:03:24: #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 06:03:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:24: #3 Pre-compute pvalue-qvalue table... 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 06:03:27: 3000000 INFO @ Sat, 03 Apr 2021 06:03:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.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 06:03:28: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:28: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:37: 4000000 INFO @ Sat, 03 Apr 2021 06:03:37: 1000000 INFO @ Sat, 03 Apr 2021 06:03:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:46: 5000000 INFO @ Sat, 03 Apr 2021 06:03:47: 2000000 INFO @ Sat, 03 Apr 2021 06:03:55: 6000000 INFO @ Sat, 03 Apr 2021 06:03:56: 3000000 INFO @ Sat, 03 Apr 2021 06:03:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.05_summits.bed INFO @ Sat, 03 Apr 2021 06:03:59: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (20190 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:04:04: 7000000 INFO @ Sat, 03 Apr 2021 06:04:06: 4000000 INFO @ Sat, 03 Apr 2021 06:04:07: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:04:07: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:04:07: #1 total tags in treatment: 7348750 INFO @ Sat, 03 Apr 2021 06:04:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:07: #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 06:04:07: #1 tags after filtering in treatment: 7348750 INFO @ Sat, 03 Apr 2021 06:04:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:07: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:08: #2 number of paired peaks: 4043 INFO @ Sat, 03 Apr 2021 06:04:08: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:08: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:08: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:08: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:08: #2 predicted fragment length is 81 bps INFO @ Sat, 03 Apr 2021 06:04:08: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 03 Apr 2021 06:04:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.10_model.r WARNING @ Sat, 03 Apr 2021 06:04:08: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:08: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 03 Apr 2021 06:04:08: #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 06:04:08: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:15: 5000000 INFO @ Sat, 03 Apr 2021 06:04:25: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:04:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:33: 7000000 INFO @ Sat, 03 Apr 2021 06:04:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:04:36: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:04:36: #1 total tags in treatment: 7348750 INFO @ Sat, 03 Apr 2021 06:04:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:36: #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 06:04:37: #1 tags after filtering in treatment: 7348750 INFO @ Sat, 03 Apr 2021 06:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:38: #2 number of paired peaks: 4043 INFO @ Sat, 03 Apr 2021 06:04:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:38: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:38: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:38: #2 predicted fragment length is 81 bps INFO @ Sat, 03 Apr 2021 06:04:38: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 03 Apr 2021 06:04:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.20_model.r WARNING @ Sat, 03 Apr 2021 06:04:38: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:38: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 03 Apr 2021 06:04:38: #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 06:04:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.10_summits.bed INFO @ Sat, 03 Apr 2021 06:04:43: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12055 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:05:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:05:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:05:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:05:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032284/SRX3032284.20_summits.bed INFO @ Sat, 03 Apr 2021 06:05:12: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4200 records, 4 fields): 12 millis CompletedMACS2peakCalling