Job ID = 12266592 SRX = SRX7282928 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19674377 spots for SRR10603287/SRR10603287.sra Written 19674377 spots for SRR10603287/SRR10603287.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266831 ("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: 00:05:04 19674377 reads; of these: 19674377 (100.00%) were unpaired; of these: 2984043 (15.17%) aligned 0 times 15108763 (76.79%) aligned exactly 1 time 1581571 (8.04%) aligned >1 times 84.83% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 8233538 / 16690334 = 0.4933 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 09:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.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 09:11:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:11:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:11:15: 1000000 INFO @ Sat, 03 Apr 2021 09:11:21: 2000000 INFO @ Sat, 03 Apr 2021 09:11:26: 3000000 INFO @ Sat, 03 Apr 2021 09:11:31: 4000000 INFO @ Sat, 03 Apr 2021 09:11:36: 5000000 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 09:11:41: 6000000 INFO @ Sat, 03 Apr 2021 09:11:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.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 09:11:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:11:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:11:46: 7000000 INFO @ Sat, 03 Apr 2021 09:11:47: 1000000 INFO @ Sat, 03 Apr 2021 09:11:52: 8000000 INFO @ Sat, 03 Apr 2021 09:11:54: 2000000 INFO @ Sat, 03 Apr 2021 09:11:55: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 09:11:55: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 09:11:55: #1 total tags in treatment: 8456796 INFO @ Sat, 03 Apr 2021 09:11:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:11:55: #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 09:11:55: #1 tags after filtering in treatment: 8456796 INFO @ Sat, 03 Apr 2021 09:11:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 09:11:55: #1 finished! INFO @ Sat, 03 Apr 2021 09:11:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:11:56: #2 number of paired peaks: 4659 INFO @ Sat, 03 Apr 2021 09:11:56: start model_add_line... INFO @ Sat, 03 Apr 2021 09:11:56: start X-correlation... INFO @ Sat, 03 Apr 2021 09:11:56: end of X-cor INFO @ Sat, 03 Apr 2021 09:11:56: #2 finished! INFO @ Sat, 03 Apr 2021 09:11:56: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 09:11:56: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 03 Apr 2021 09:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.05_model.r WARNING @ Sat, 03 Apr 2021 09:11:56: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:11:56: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 03 Apr 2021 09:11:56: #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 09:11:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:12:00: 3000000 INFO @ Sat, 03 Apr 2021 09:12:06: 4000000 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 09:12:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.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 09:12:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:12:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:12:12: 5000000 INFO @ Sat, 03 Apr 2021 09:12:16: 1000000 INFO @ Sat, 03 Apr 2021 09:12:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:12:19: 6000000 INFO @ Sat, 03 Apr 2021 09:12:23: 2000000 INFO @ Sat, 03 Apr 2021 09:12:25: 7000000 INFO @ Sat, 03 Apr 2021 09:12:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:12:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:12:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.05_summits.bed INFO @ Sat, 03 Apr 2021 09:12:30: Done! INFO @ Sat, 03 Apr 2021 09:12:30: 3000000 pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (23382 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:12:31: 8000000 INFO @ Sat, 03 Apr 2021 09:12:34: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 09:12:34: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 09:12:34: #1 total tags in treatment: 8456796 INFO @ Sat, 03 Apr 2021 09:12:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:12:34: #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 09:12:35: #1 tags after filtering in treatment: 8456796 INFO @ Sat, 03 Apr 2021 09:12:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 09:12:35: #1 finished! INFO @ Sat, 03 Apr 2021 09:12:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:12:36: #2 number of paired peaks: 4659 INFO @ Sat, 03 Apr 2021 09:12:36: start model_add_line... INFO @ Sat, 03 Apr 2021 09:12:36: start X-correlation... INFO @ Sat, 03 Apr 2021 09:12:36: end of X-cor INFO @ Sat, 03 Apr 2021 09:12:36: #2 finished! INFO @ Sat, 03 Apr 2021 09:12:36: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 09:12:36: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 03 Apr 2021 09:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.10_model.r WARNING @ Sat, 03 Apr 2021 09:12:36: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:12:36: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 03 Apr 2021 09:12:36: #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 09:12:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:12:36: 4000000 INFO @ Sat, 03 Apr 2021 09:12:43: 5000000 INFO @ Sat, 03 Apr 2021 09:12:49: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:12:55: 7000000 INFO @ Sat, 03 Apr 2021 09:12:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:13:01: 8000000 INFO @ Sat, 03 Apr 2021 09:13:04: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 09:13:04: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 09:13:04: #1 total tags in treatment: 8456796 INFO @ Sat, 03 Apr 2021 09:13:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:13:04: #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 09:13:04: #1 tags after filtering in treatment: 8456796 INFO @ Sat, 03 Apr 2021 09:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 09:13:04: #1 finished! INFO @ Sat, 03 Apr 2021 09:13:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:13:05: #2 number of paired peaks: 4659 INFO @ Sat, 03 Apr 2021 09:13:05: start model_add_line... INFO @ Sat, 03 Apr 2021 09:13:06: start X-correlation... INFO @ Sat, 03 Apr 2021 09:13:06: end of X-cor INFO @ Sat, 03 Apr 2021 09:13:06: #2 finished! INFO @ Sat, 03 Apr 2021 09:13:06: #2 predicted fragment length is 76 bps INFO @ Sat, 03 Apr 2021 09:13:06: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 03 Apr 2021 09:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.20_model.r WARNING @ Sat, 03 Apr 2021 09:13:06: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:13:06: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 03 Apr 2021 09:13:06: #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 09:13:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.10_summits.bed INFO @ Sat, 03 Apr 2021 09:13:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (14839 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:13:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:13:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:13:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:13:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282928/SRX7282928.20_summits.bed INFO @ Sat, 03 Apr 2021 09:13:38: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6442 records, 4 fields): 8 millis CompletedMACS2peakCalling