Job ID = 12264876 SRX = SRX3032275 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15054106 spots for SRR5863965/SRR5863965.sra Written 15054106 spots for SRR5863965/SRR5863965.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265052 ("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: 00:03:50 15054106 reads; of these: 15054106 (100.00%) were unpaired; of these: 1989308 (13.21%) aligned 0 times 11144862 (74.03%) aligned exactly 1 time 1919936 (12.75%) aligned >1 times 86.79% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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] 5316661 / 13064798 = 0.4069 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 06:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.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 06:02:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:25: 1000000 INFO @ Sat, 03 Apr 2021 06:02:34: 2000000 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 06:02:43: 3000000 INFO @ Sat, 03 Apr 2021 06:02:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.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 06:02:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:53: 4000000 INFO @ Sat, 03 Apr 2021 06:02:55: 1000000 INFO @ Sat, 03 Apr 2021 06:03:03: 5000000 INFO @ Sat, 03 Apr 2021 06:03:05: 2000000 INFO @ Sat, 03 Apr 2021 06:03:12: 6000000 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 06:03:15: 3000000 INFO @ Sat, 03 Apr 2021 06:03:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.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 06:03:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:22: 7000000 INFO @ Sat, 03 Apr 2021 06:03:25: 4000000 INFO @ Sat, 03 Apr 2021 06:03:25: 1000000 INFO @ Sat, 03 Apr 2021 06:03:29: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:03:29: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:03:29: #1 total tags in treatment: 7748137 INFO @ Sat, 03 Apr 2021 06:03:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:29: #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 06:03:29: #1 tags after filtering in treatment: 7748137 INFO @ Sat, 03 Apr 2021 06:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:29: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:30: #2 number of paired peaks: 4251 INFO @ Sat, 03 Apr 2021 06:03:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:30: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:30: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:30: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 06:03:30: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 03 Apr 2021 06:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.05_model.r WARNING @ Sat, 03 Apr 2021 06:03:30: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:03:30: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 03 Apr 2021 06:03:30: #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 06:03:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:35: 2000000 INFO @ Sat, 03 Apr 2021 06:03:35: 5000000 INFO @ Sat, 03 Apr 2021 06:03:44: 3000000 INFO @ Sat, 03 Apr 2021 06:03:44: 6000000 INFO @ Sat, 03 Apr 2021 06:03:53: 4000000 INFO @ Sat, 03 Apr 2021 06:03:54: 7000000 INFO @ Sat, 03 Apr 2021 06:03:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:04:01: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:04:01: #1 total tags in treatment: 7748137 INFO @ Sat, 03 Apr 2021 06:04:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:01: #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 06:04:01: #1 tags after filtering in treatment: 7748137 INFO @ Sat, 03 Apr 2021 06:04:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:01: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:02: #2 number of paired peaks: 4251 INFO @ Sat, 03 Apr 2021 06:04:02: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:02: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:02: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:02: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:02: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 06:04:02: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 03 Apr 2021 06:04:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.10_model.r WARNING @ Sat, 03 Apr 2021 06:04:02: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:02: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 03 Apr 2021 06:04:02: #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 06:04:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:03: 5000000 INFO @ Sat, 03 Apr 2021 06:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.05_summits.bed INFO @ Sat, 03 Apr 2021 06:04:10: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (18814 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:04:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:04:21: 7000000 INFO @ Sat, 03 Apr 2021 06:04:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:04:27: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:04:27: #1 total tags in treatment: 7748137 INFO @ Sat, 03 Apr 2021 06:04:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:27: #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 06:04:28: #1 tags after filtering in treatment: 7748137 INFO @ Sat, 03 Apr 2021 06:04:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:28: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:29: #2 number of paired peaks: 4251 INFO @ Sat, 03 Apr 2021 06:04:29: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:29: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:29: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:29: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:29: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 06:04:29: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 03 Apr 2021 06:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.20_model.r WARNING @ Sat, 03 Apr 2021 06:04:29: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:29: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 03 Apr 2021 06:04:29: #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 06:04:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.10_summits.bed INFO @ Sat, 03 Apr 2021 06:04:38: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11401 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:04:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:05:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:05:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032275/SRX3032275.20_summits.bed INFO @ Sat, 03 Apr 2021 06:05:06: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4604 records, 4 fields): 11 millis CompletedMACS2peakCalling