Job ID = 12264871 SRX = SRX3032270 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19552861 spots for SRR5863960/SRR5863960.sra Written 19552861 spots for SRR5863960/SRR5863960.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265087 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:52 19552861 reads; of these: 19552861 (100.00%) were unpaired; of these: 2971496 (15.20%) aligned 0 times 13872847 (70.95%) aligned exactly 1 time 2708518 (13.85%) aligned >1 times 84.80% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7422583 / 16581365 = 0.4476 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 06:05:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.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 06:05:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:05:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:05:14: 1000000 INFO @ Sat, 03 Apr 2021 06:05:21: 2000000 INFO @ Sat, 03 Apr 2021 06:05:27: 3000000 INFO @ Sat, 03 Apr 2021 06:05:34: 4000000 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 06:05:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.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 06:05:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:05:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:05:41: 5000000 INFO @ Sat, 03 Apr 2021 06:05:47: 1000000 INFO @ Sat, 03 Apr 2021 06:05:48: 6000000 INFO @ Sat, 03 Apr 2021 06:05:54: 7000000 INFO @ Sat, 03 Apr 2021 06:05:55: 2000000 INFO @ Sat, 03 Apr 2021 06:06:02: 8000000 INFO @ Sat, 03 Apr 2021 06:06:03: 3000000 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 06:06:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.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 06:06:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:10: 9000000 INFO @ Sat, 03 Apr 2021 06:06:11: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:06:11: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:06:11: #1 total tags in treatment: 9158782 INFO @ Sat, 03 Apr 2021 06:06:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:06:11: #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 06:06:11: #1 tags after filtering in treatment: 9158782 INFO @ Sat, 03 Apr 2021 06:06:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:06:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:06:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:06:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:06:12: 4000000 INFO @ Sat, 03 Apr 2021 06:06:12: #2 number of paired peaks: 3414 INFO @ Sat, 03 Apr 2021 06:06:12: start model_add_line... INFO @ Sat, 03 Apr 2021 06:06:12: start X-correlation... INFO @ Sat, 03 Apr 2021 06:06:12: end of X-cor INFO @ Sat, 03 Apr 2021 06:06:12: #2 finished! INFO @ Sat, 03 Apr 2021 06:06:12: #2 predicted fragment length is 80 bps INFO @ Sat, 03 Apr 2021 06:06:12: #2 alternative fragment length(s) may be 80 bps INFO @ Sat, 03 Apr 2021 06:06:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.05_model.r WARNING @ Sat, 03 Apr 2021 06:06:12: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:06:12: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sat, 03 Apr 2021 06:06:12: #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 06:06:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:06:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:06:16: 1000000 INFO @ Sat, 03 Apr 2021 06:06:21: 5000000 INFO @ Sat, 03 Apr 2021 06:06:25: 2000000 INFO @ Sat, 03 Apr 2021 06:06:30: 6000000 INFO @ Sat, 03 Apr 2021 06:06:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:06:33: 3000000 INFO @ Sat, 03 Apr 2021 06:06:39: 7000000 INFO @ Sat, 03 Apr 2021 06:06:41: 4000000 INFO @ Sat, 03 Apr 2021 06:06:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:06:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:06:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.05_summits.bed INFO @ Sat, 03 Apr 2021 06:06:43: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (21444 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:06:48: 8000000 INFO @ Sat, 03 Apr 2021 06:06:49: 5000000 INFO @ Sat, 03 Apr 2021 06:06:56: 6000000 INFO @ Sat, 03 Apr 2021 06:06:58: 9000000 INFO @ Sat, 03 Apr 2021 06:06:59: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:06:59: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:06:59: #1 total tags in treatment: 9158782 INFO @ Sat, 03 Apr 2021 06:06:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:06:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:06:59: #1 tags after filtering in treatment: 9158782 INFO @ Sat, 03 Apr 2021 06:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:06:59: #1 finished! INFO @ Sat, 03 Apr 2021 06:06:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:00: #2 number of paired peaks: 3414 INFO @ Sat, 03 Apr 2021 06:07:00: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:00: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:00: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:00: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:00: #2 predicted fragment length is 80 bps INFO @ Sat, 03 Apr 2021 06:07:00: #2 alternative fragment length(s) may be 80 bps INFO @ Sat, 03 Apr 2021 06:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.10_model.r WARNING @ Sat, 03 Apr 2021 06:07:00: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:00: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sat, 03 Apr 2021 06:07:00: #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 06:07:00: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:07:05: 7000000 INFO @ Sat, 03 Apr 2021 06:07:13: 8000000 INFO @ Sat, 03 Apr 2021 06:07:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:07:20: 9000000 INFO @ Sat, 03 Apr 2021 06:07:21: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:07:21: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:07:21: #1 total tags in treatment: 9158782 INFO @ Sat, 03 Apr 2021 06:07:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:21: #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 06:07:21: #1 tags after filtering in treatment: 9158782 INFO @ Sat, 03 Apr 2021 06:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:07:21: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:22: #2 number of paired peaks: 3414 INFO @ Sat, 03 Apr 2021 06:07:22: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:22: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:22: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:22: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:22: #2 predicted fragment length is 80 bps INFO @ Sat, 03 Apr 2021 06:07:22: #2 alternative fragment length(s) may be 80 bps INFO @ Sat, 03 Apr 2021 06:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.20_model.r WARNING @ Sat, 03 Apr 2021 06:07:22: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:22: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sat, 03 Apr 2021 06:07:22: #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 06:07:22: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.10_summits.bed INFO @ Sat, 03 Apr 2021 06:07:31: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12810 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:07:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:07:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:07:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032270/SRX3032270.20_summits.bed INFO @ Sat, 03 Apr 2021 06:07:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4897 records, 4 fields): 8 millis CompletedMACS2peakCalling