Job ID = 12264865 SRX = SRX3032264 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15571259 spots for SRR5863954/SRR5863954.sra Written 15571259 spots for SRR5863954/SRR5863954.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265102 ("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: 00:06:38 15571259 reads; of these: 15571259 (100.00%) were unpaired; of these: 4068370 (26.13%) aligned 0 times 9728190 (62.48%) aligned exactly 1 time 1774699 (11.40%) aligned >1 times 73.87% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 4117023 / 11502889 = 0.3579 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 06:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.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 06:06:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:41: 1000000 INFO @ Sat, 03 Apr 2021 06:06:49: 2000000 INFO @ Sat, 03 Apr 2021 06:06:57: 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 06:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.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 06:07:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:05: 4000000 INFO @ Sat, 03 Apr 2021 06:07:12: 1000000 INFO @ Sat, 03 Apr 2021 06:07:13: 5000000 INFO @ Sat, 03 Apr 2021 06:07:21: 6000000 INFO @ Sat, 03 Apr 2021 06:07:21: 2000000 INFO @ Sat, 03 Apr 2021 06:07:30: 7000000 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 06:07:31: 3000000 INFO @ Sat, 03 Apr 2021 06:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.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 06:07:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:33: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:07:33: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:07:33: #1 total tags in treatment: 7385866 INFO @ Sat, 03 Apr 2021 06:07:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:33: #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 06:07:33: #1 tags after filtering in treatment: 7385866 INFO @ Sat, 03 Apr 2021 06:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:07:33: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:34: #2 number of paired peaks: 3343 INFO @ Sat, 03 Apr 2021 06:07:34: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:34: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:34: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:34: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:34: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 06:07:34: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 03 Apr 2021 06:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.05_model.r WARNING @ Sat, 03 Apr 2021 06:07:34: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:34: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 03 Apr 2021 06:07:34: #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 06:07:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:07:40: 4000000 INFO @ Sat, 03 Apr 2021 06:07:41: 1000000 INFO @ Sat, 03 Apr 2021 06:07:48: 2000000 INFO @ Sat, 03 Apr 2021 06:07:49: 5000000 INFO @ Sat, 03 Apr 2021 06:07:56: 3000000 INFO @ Sat, 03 Apr 2021 06:07:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:07:58: 6000000 INFO @ Sat, 03 Apr 2021 06:08:03: 4000000 INFO @ Sat, 03 Apr 2021 06:08:07: 7000000 INFO @ Sat, 03 Apr 2021 06:08:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.05_summits.bed INFO @ Sat, 03 Apr 2021 06:08:10: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (15429 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:08:10: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:08:10: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:08:10: #1 total tags in treatment: 7385866 INFO @ Sat, 03 Apr 2021 06:08:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:10: #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 06:08:11: #1 tags after filtering in treatment: 7385866 INFO @ Sat, 03 Apr 2021 06:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:08:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:11: 5000000 INFO @ Sat, 03 Apr 2021 06:08:12: #2 number of paired peaks: 3343 INFO @ Sat, 03 Apr 2021 06:08:12: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:12: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:12: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:12: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:12: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 06:08:12: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 03 Apr 2021 06:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.10_model.r WARNING @ Sat, 03 Apr 2021 06:08:12: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:12: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 03 Apr 2021 06:08:12: #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 06:08:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:18: 6000000 INFO @ Sat, 03 Apr 2021 06:08:25: 7000000 INFO @ Sat, 03 Apr 2021 06:08:28: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:08:28: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:08:28: #1 total tags in treatment: 7385866 INFO @ Sat, 03 Apr 2021 06:08:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:28: #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 06:08:28: #1 tags after filtering in treatment: 7385866 INFO @ Sat, 03 Apr 2021 06:08:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:08:28: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:29: #2 number of paired peaks: 3343 INFO @ Sat, 03 Apr 2021 06:08:29: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:30: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:30: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:30: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 06:08:30: #2 alternative fragment length(s) may be 99 bps INFO @ Sat, 03 Apr 2021 06:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.20_model.r WARNING @ Sat, 03 Apr 2021 06:08:30: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:30: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Sat, 03 Apr 2021 06:08:30: #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 06:08:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:34: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:08:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.10_summits.bed INFO @ Sat, 03 Apr 2021 06:08:47: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9735 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:08:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032264/SRX3032264.20_summits.bed INFO @ Sat, 03 Apr 2021 06:09:03: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3975 records, 4 fields): 12 millis CompletedMACS2peakCalling