Job ID = 14171064 SRX = SRX10000685 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14627940 spots for SRR13606612/SRR13606612.sra Written 14627940 spots for SRR13606612/SRR13606612.sra Read 14133771 spots for SRR13606613/SRR13606613.sra Written 14133771 spots for SRR13606613/SRR13606613.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171510 ("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: 00:07:07 28761711 reads; of these: 28761711 (100.00%) were unpaired; of these: 26987102 (93.83%) aligned 0 times 1227659 (4.27%) aligned exactly 1 time 546950 (1.90%) aligned >1 times 6.17% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 252773 / 1774609 = 0.1424 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.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, 11 Dec 2021 09:28:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:28:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:28:51: 1000000 INFO @ Sat, 11 Dec 2021 09:28:56: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:28:56: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:28:56: #1 total tags in treatment: 1521836 INFO @ Sat, 11 Dec 2021 09:28:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:28:56: #1 tags after filtering in treatment: 1521836 INFO @ Sat, 11 Dec 2021 09:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:28:56: #1 finished! INFO @ Sat, 11 Dec 2021 09:28:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:28:56: #2 number of paired peaks: 1312 INFO @ Sat, 11 Dec 2021 09:28:56: start model_add_line... INFO @ Sat, 11 Dec 2021 09:28:56: start X-correlation... INFO @ Sat, 11 Dec 2021 09:28:56: end of X-cor INFO @ Sat, 11 Dec 2021 09:28:56: #2 finished! INFO @ Sat, 11 Dec 2021 09:28:56: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 09:28:56: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 09:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.05_model.r WARNING @ Sat, 11 Dec 2021 09:28:56: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:28:56: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 11 Dec 2021 09:28:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:28:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:29:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:29:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:29:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:29:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.05_summits.bed INFO @ Sat, 11 Dec 2021 09:29:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (767 records, 4 fields): 3 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.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, 11 Dec 2021 09:29:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:29:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:29:20: 1000000 INFO @ Sat, 11 Dec 2021 09:29:26: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:29:26: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:29:26: #1 total tags in treatment: 1521836 INFO @ Sat, 11 Dec 2021 09:29:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:29:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:29:26: #1 tags after filtering in treatment: 1521836 INFO @ Sat, 11 Dec 2021 09:29:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:29:26: #1 finished! INFO @ Sat, 11 Dec 2021 09:29:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:29:26: #2 number of paired peaks: 1312 INFO @ Sat, 11 Dec 2021 09:29:26: start model_add_line... INFO @ Sat, 11 Dec 2021 09:29:26: start X-correlation... INFO @ Sat, 11 Dec 2021 09:29:26: end of X-cor INFO @ Sat, 11 Dec 2021 09:29:26: #2 finished! INFO @ Sat, 11 Dec 2021 09:29:26: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 09:29:26: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 09:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.10_model.r WARNING @ Sat, 11 Dec 2021 09:29:26: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:29:26: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 11 Dec 2021 09:29:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:29:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:29:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.10_summits.bed INFO @ Sat, 11 Dec 2021 09:29:34: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.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, 11 Dec 2021 09:29:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:29:39: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:29:50: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:29:55: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:29:55: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:29:55: #1 total tags in treatment: 1521836 INFO @ Sat, 11 Dec 2021 09:29:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:29:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:29:55: #1 tags after filtering in treatment: 1521836 INFO @ Sat, 11 Dec 2021 09:29:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:29:55: #1 finished! INFO @ Sat, 11 Dec 2021 09:29:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:29:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:29:56: #2 number of paired peaks: 1312 INFO @ Sat, 11 Dec 2021 09:29:56: start model_add_line... INFO @ Sat, 11 Dec 2021 09:29:56: start X-correlation... INFO @ Sat, 11 Dec 2021 09:29:56: end of X-cor INFO @ Sat, 11 Dec 2021 09:29:56: #2 finished! INFO @ Sat, 11 Dec 2021 09:29:56: #2 predicted fragment length is 97 bps INFO @ Sat, 11 Dec 2021 09:29:56: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 11 Dec 2021 09:29:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.20_model.r WARNING @ Sat, 11 Dec 2021 09:29:56: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:29:56: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 11 Dec 2021 09:29:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:29:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:29:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:30:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:30:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:30:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:30:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000685/SRX10000685.20_summits.bed INFO @ Sat, 11 Dec 2021 09:30:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (115 records, 4 fields): 1 millis CompletedMACS2peakCalling