Job ID = 12265198 SRX = SRX3467362 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20852076 spots for SRR6372040/SRR6372040.sra Written 20852076 spots for SRR6372040/SRR6372040.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265376 ("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: 00:07:53 20852076 reads; of these: 20852076 (100.00%) were unpaired; of these: 12970684 (62.20%) aligned 0 times 6996016 (33.55%) aligned exactly 1 time 885376 (4.25%) aligned >1 times 37.80% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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] 2659365 / 7881392 = 0.3374 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 06:24:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.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 06:24:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:24:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:24:29: 1000000 INFO @ Sat, 03 Apr 2021 06:24:37: 2000000 INFO @ Sat, 03 Apr 2021 06:24:45: 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 06:24:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.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 06:24:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:24:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:24:54: 4000000 INFO @ Sat, 03 Apr 2021 06:25:02: 1000000 INFO @ Sat, 03 Apr 2021 06:25:04: 5000000 INFO @ Sat, 03 Apr 2021 06:25:07: #1 tag size is determined as 97 bps INFO @ Sat, 03 Apr 2021 06:25:07: #1 tag size = 97 INFO @ Sat, 03 Apr 2021 06:25:07: #1 total tags in treatment: 5222027 INFO @ Sat, 03 Apr 2021 06:25:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:25:07: #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 06:25:07: #1 tags after filtering in treatment: 5222027 INFO @ Sat, 03 Apr 2021 06:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:25:07: #1 finished! INFO @ Sat, 03 Apr 2021 06:25:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:25:08: #2 number of paired peaks: 5131 INFO @ Sat, 03 Apr 2021 06:25:08: start model_add_line... INFO @ Sat, 03 Apr 2021 06:25:08: start X-correlation... INFO @ Sat, 03 Apr 2021 06:25:08: end of X-cor INFO @ Sat, 03 Apr 2021 06:25:08: #2 finished! INFO @ Sat, 03 Apr 2021 06:25:08: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Apr 2021 06:25:08: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Apr 2021 06:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.05_model.r WARNING @ Sat, 03 Apr 2021 06:25:08: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:25:08: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Sat, 03 Apr 2021 06:25:08: #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 06:25:08: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:25:12: 2000000 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 06:25:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.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 06:25:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:25:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:25:22: 3000000 INFO @ Sat, 03 Apr 2021 06:25:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:25:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:25:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.05_summits.bed INFO @ Sat, 03 Apr 2021 06:25:28: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (17614 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:25:32: 1000000 INFO @ Sat, 03 Apr 2021 06:25:33: 4000000 INFO @ Sat, 03 Apr 2021 06:25:43: 2000000 INFO @ Sat, 03 Apr 2021 06:25:44: 5000000 INFO @ Sat, 03 Apr 2021 06:25:47: #1 tag size is determined as 97 bps INFO @ Sat, 03 Apr 2021 06:25:47: #1 tag size = 97 INFO @ Sat, 03 Apr 2021 06:25:47: #1 total tags in treatment: 5222027 INFO @ Sat, 03 Apr 2021 06:25:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:25:47: #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 06:25:47: #1 tags after filtering in treatment: 5222027 INFO @ Sat, 03 Apr 2021 06:25:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:25:47: #1 finished! INFO @ Sat, 03 Apr 2021 06:25:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:25:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:25:47: #2 number of paired peaks: 5131 INFO @ Sat, 03 Apr 2021 06:25:47: start model_add_line... INFO @ Sat, 03 Apr 2021 06:25:47: start X-correlation... INFO @ Sat, 03 Apr 2021 06:25:47: end of X-cor INFO @ Sat, 03 Apr 2021 06:25:47: #2 finished! INFO @ Sat, 03 Apr 2021 06:25:47: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Apr 2021 06:25:47: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Apr 2021 06:25:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.10_model.r WARNING @ Sat, 03 Apr 2021 06:25:47: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:25:47: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Sat, 03 Apr 2021 06:25:47: #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 06:25:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:25:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:25:52: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:26:01: 4000000 INFO @ Sat, 03 Apr 2021 06:26:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.10_summits.bed INFO @ Sat, 03 Apr 2021 06:26:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10810 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:26:09: 5000000 INFO @ Sat, 03 Apr 2021 06:26:11: #1 tag size is determined as 97 bps INFO @ Sat, 03 Apr 2021 06:26:11: #1 tag size = 97 INFO @ Sat, 03 Apr 2021 06:26:11: #1 total tags in treatment: 5222027 INFO @ Sat, 03 Apr 2021 06:26:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:26:11: #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 06:26:11: #1 tags after filtering in treatment: 5222027 INFO @ Sat, 03 Apr 2021 06:26:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:26:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:26:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:26:12: #2 number of paired peaks: 5131 INFO @ Sat, 03 Apr 2021 06:26:12: start model_add_line... INFO @ Sat, 03 Apr 2021 06:26:12: start X-correlation... INFO @ Sat, 03 Apr 2021 06:26:12: end of X-cor INFO @ Sat, 03 Apr 2021 06:26:12: #2 finished! INFO @ Sat, 03 Apr 2021 06:26:12: #2 predicted fragment length is 116 bps INFO @ Sat, 03 Apr 2021 06:26:12: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 03 Apr 2021 06:26:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.20_model.r WARNING @ Sat, 03 Apr 2021 06:26:12: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:26:12: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Sat, 03 Apr 2021 06:26:12: #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 06:26:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:26:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:26:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:26:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:26:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3467362/SRX3467362.20_summits.bed INFO @ Sat, 03 Apr 2021 06:26:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4785 records, 4 fields): 7 millis CompletedMACS2peakCalling