Job ID = 12264863 SRX = SRX3032262 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17597420 spots for SRR5863952/SRR5863952.sra Written 17597420 spots for SRR5863952/SRR5863952.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265065 ("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: 00:05:17 17597420 reads; of these: 17597420 (100.00%) were unpaired; of these: 4255264 (24.18%) aligned 0 times 11000540 (62.51%) aligned exactly 1 time 2341616 (13.31%) aligned >1 times 75.82% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 4532336 / 13342156 = 0.3397 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 06:03:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.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 06:03:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:54: 1000000 INFO @ Sat, 03 Apr 2021 06:04:03: 2000000 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 06:04:12: 3000000 INFO @ Sat, 03 Apr 2021 06:04:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.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 06:04:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:22: 4000000 INFO @ Sat, 03 Apr 2021 06:04:25: 1000000 INFO @ Sat, 03 Apr 2021 06:04:31: 5000000 INFO @ Sat, 03 Apr 2021 06:04:37: 2000000 BedGraph に変換中... INFO @ Sat, 03 Apr 2021 06:04:41: 6000000 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 06:04:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.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 06:04:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:48: 3000000 INFO @ Sat, 03 Apr 2021 06:04:50: 7000000 INFO @ Sat, 03 Apr 2021 06:04:53: 1000000 INFO @ Sat, 03 Apr 2021 06:04:59: 4000000 INFO @ Sat, 03 Apr 2021 06:05:00: 8000000 INFO @ Sat, 03 Apr 2021 06:05:03: 2000000 INFO @ Sat, 03 Apr 2021 06:05:08: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:05:08: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:05:08: #1 total tags in treatment: 8809820 INFO @ Sat, 03 Apr 2021 06:05:08: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:05:08: #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 06:05:08: #1 tags after filtering in treatment: 8809820 INFO @ Sat, 03 Apr 2021 06:05:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:05:08: #1 finished! INFO @ Sat, 03 Apr 2021 06:05:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:05:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:05:09: #2 number of paired peaks: 2092 INFO @ Sat, 03 Apr 2021 06:05:09: start model_add_line... INFO @ Sat, 03 Apr 2021 06:05:09: start X-correlation... INFO @ Sat, 03 Apr 2021 06:05:09: end of X-cor INFO @ Sat, 03 Apr 2021 06:05:09: #2 finished! INFO @ Sat, 03 Apr 2021 06:05:09: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 06:05:09: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Apr 2021 06:05:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.05_model.r WARNING @ Sat, 03 Apr 2021 06:05:09: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:05:09: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Apr 2021 06:05:09: #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 06:05:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:05:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:05:11: 5000000 INFO @ Sat, 03 Apr 2021 06:05:12: 3000000 INFO @ Sat, 03 Apr 2021 06:05:21: 4000000 INFO @ Sat, 03 Apr 2021 06:05:22: 6000000 INFO @ Sat, 03 Apr 2021 06:05:31: 5000000 INFO @ Sat, 03 Apr 2021 06:05:33: 7000000 INFO @ Sat, 03 Apr 2021 06:05:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:05:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:05:45: 8000000 INFO @ Sat, 03 Apr 2021 06:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.05_summits.bed INFO @ Sat, 03 Apr 2021 06:05:49: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16073 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:05:50: 7000000 INFO @ Sat, 03 Apr 2021 06:05:54: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:05:54: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:05:54: #1 total tags in treatment: 8809820 INFO @ Sat, 03 Apr 2021 06:05:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:05:54: #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 06:05:54: #1 tags after filtering in treatment: 8809820 INFO @ Sat, 03 Apr 2021 06:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:05:54: #1 finished! INFO @ Sat, 03 Apr 2021 06:05:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:05:55: #2 number of paired peaks: 2092 INFO @ Sat, 03 Apr 2021 06:05:55: start model_add_line... INFO @ Sat, 03 Apr 2021 06:05:55: start X-correlation... INFO @ Sat, 03 Apr 2021 06:05:55: end of X-cor INFO @ Sat, 03 Apr 2021 06:05:55: #2 finished! INFO @ Sat, 03 Apr 2021 06:05:55: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 06:05:55: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Apr 2021 06:05:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.10_model.r WARNING @ Sat, 03 Apr 2021 06:05:55: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:05:55: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Apr 2021 06:05:55: #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 06:05:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:05:59: 8000000 INFO @ Sat, 03 Apr 2021 06:06:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:06:06: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:06:06: #1 total tags in treatment: 8809820 INFO @ Sat, 03 Apr 2021 06:06:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:06:06: #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 06:06:06: #1 tags after filtering in treatment: 8809820 INFO @ Sat, 03 Apr 2021 06:06:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:06:06: #1 finished! INFO @ Sat, 03 Apr 2021 06:06:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:06:07: #2 number of paired peaks: 2092 INFO @ Sat, 03 Apr 2021 06:06:07: start model_add_line... INFO @ Sat, 03 Apr 2021 06:06:07: start X-correlation... INFO @ Sat, 03 Apr 2021 06:06:07: end of X-cor INFO @ Sat, 03 Apr 2021 06:06:07: #2 finished! INFO @ Sat, 03 Apr 2021 06:06:07: #2 predicted fragment length is 85 bps INFO @ Sat, 03 Apr 2021 06:06:07: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 03 Apr 2021 06:06:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.20_model.r WARNING @ Sat, 03 Apr 2021 06:06:07: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:06:07: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 03 Apr 2021 06:06:07: #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 06:06:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:06:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:06:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:06:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:06:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:06:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:06:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.10_summits.bed INFO @ Sat, 03 Apr 2021 06:06:34: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8882 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032262/SRX3032262.20_summits.bed INFO @ Sat, 03 Apr 2021 06:06:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2841 records, 4 fields): 5 millis CompletedMACS2peakCalling