Job ID = 12265200 SRX = SRX3467364 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8161317 spots for SRR6372042/SRR6372042.sra Written 8161317 spots for SRR6372042/SRR6372042.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265346 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:34 8161317 reads; of these: 8161317 (100.00%) were unpaired; of these: 4930911 (60.42%) aligned 0 times 2913861 (35.70%) aligned exactly 1 time 316545 (3.88%) aligned >1 times 39.58% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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_rmdupse_core] 794480 / 3230406 = 0.2459 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 06:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.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 06:18:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:18:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:18:19: 1000000 INFO @ Sat, 03 Apr 2021 06:18:29: 2000000 INFO @ Sat, 03 Apr 2021 06:18:33: #1 tag size is determined as 97 bps INFO @ Sat, 03 Apr 2021 06:18:33: #1 tag size = 97 INFO @ Sat, 03 Apr 2021 06:18:33: #1 total tags in treatment: 2435926 INFO @ Sat, 03 Apr 2021 06:18:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:18:33: #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 06:18:33: #1 tags after filtering in treatment: 2435926 INFO @ Sat, 03 Apr 2021 06:18:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:18:33: #1 finished! INFO @ Sat, 03 Apr 2021 06:18:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:18:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:18:33: #2 number of paired peaks: 7323 INFO @ Sat, 03 Apr 2021 06:18:33: start model_add_line... INFO @ Sat, 03 Apr 2021 06:18:34: start X-correlation... INFO @ Sat, 03 Apr 2021 06:18:34: end of X-cor INFO @ Sat, 03 Apr 2021 06:18:34: #2 finished! INFO @ Sat, 03 Apr 2021 06:18:34: #2 predicted fragment length is 120 bps INFO @ Sat, 03 Apr 2021 06:18:34: #2 alternative fragment length(s) may be 120 bps INFO @ Sat, 03 Apr 2021 06:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.05_model.r WARNING @ Sat, 03 Apr 2021 06:18:34: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:18:34: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sat, 03 Apr 2021 06:18:34: #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 06:18:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:18:34: #3 Pre-compute pvalue-qvalue table... 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 06:18:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.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 06:18:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:18:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:18:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:18:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:18:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.05_summits.bed INFO @ Sat, 03 Apr 2021 06:18:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11239 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:18:49: 1000000 INFO @ Sat, 03 Apr 2021 06:18:59: 2000000 INFO @ Sat, 03 Apr 2021 06:19:03: #1 tag size is determined as 97 bps INFO @ Sat, 03 Apr 2021 06:19:03: #1 tag size = 97 INFO @ Sat, 03 Apr 2021 06:19:03: #1 total tags in treatment: 2435926 INFO @ Sat, 03 Apr 2021 06:19:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:03: #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 06:19:03: #1 tags after filtering in treatment: 2435926 INFO @ Sat, 03 Apr 2021 06:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:19:03: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:04: #2 number of paired peaks: 7323 INFO @ Sat, 03 Apr 2021 06:19:04: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:04: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:04: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:04: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:04: #2 predicted fragment length is 120 bps INFO @ Sat, 03 Apr 2021 06:19:04: #2 alternative fragment length(s) may be 120 bps INFO @ Sat, 03 Apr 2021 06:19:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.10_model.r WARNING @ Sat, 03 Apr 2021 06:19:04: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:19:04: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sat, 03 Apr 2021 06:19:04: #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 06:19:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:04: #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 06:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.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 06:19:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:19:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:19:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.10_summits.bed INFO @ Sat, 03 Apr 2021 06:19:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6540 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:19:19: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:19:29: 2000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:19:34: #1 tag size is determined as 97 bps INFO @ Sat, 03 Apr 2021 06:19:34: #1 tag size = 97 INFO @ Sat, 03 Apr 2021 06:19:34: #1 total tags in treatment: 2435926 INFO @ Sat, 03 Apr 2021 06:19:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:34: #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 06:19:34: #1 tags after filtering in treatment: 2435926 INFO @ Sat, 03 Apr 2021 06:19:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:19:34: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:34: #2 number of paired peaks: 7323 INFO @ Sat, 03 Apr 2021 06:19:34: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:34: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:34: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:34: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:34: #2 predicted fragment length is 120 bps INFO @ Sat, 03 Apr 2021 06:19:34: #2 alternative fragment length(s) may be 120 bps INFO @ Sat, 03 Apr 2021 06:19:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.20_model.r WARNING @ Sat, 03 Apr 2021 06:19:34: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:19:34: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sat, 03 Apr 2021 06:19:34: #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 06:19:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:19:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:19:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:19:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:19:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3467364/SRX3467364.20_summits.bed INFO @ Sat, 03 Apr 2021 06:19:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2727 records, 4 fields): 6 millis CompletedMACS2peakCalling