Job ID = 14171948 SRX = SRX9427705 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15421941 spots for SRR12975512/SRR12975512.sra Written 15421941 spots for SRR12975512/SRR12975512.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172430 ("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: 00:07:34 15421941 reads; of these: 15421941 (100.00%) were unpaired; of these: 311364 (2.02%) aligned 0 times 4541112 (29.45%) aligned exactly 1 time 10569465 (68.54%) aligned >1 times 97.98% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 3307881 / 15110577 = 0.2189 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 13:40:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.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 13:40:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:40:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:41:00: 1000000 INFO @ Sat, 11 Dec 2021 13:41:06: 2000000 INFO @ Sat, 11 Dec 2021 13:41:12: 3000000 INFO @ Sat, 11 Dec 2021 13:41:19: 4000000 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 13:41:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.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 13:41:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:41:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:41:25: 5000000 INFO @ Sat, 11 Dec 2021 13:41:30: 1000000 INFO @ Sat, 11 Dec 2021 13:41:31: 6000000 INFO @ Sat, 11 Dec 2021 13:41:36: 2000000 INFO @ Sat, 11 Dec 2021 13:41:37: 7000000 INFO @ Sat, 11 Dec 2021 13:41:42: 3000000 INFO @ Sat, 11 Dec 2021 13:41:44: 8000000 INFO @ Sat, 11 Dec 2021 13:41:47: 4000000 INFO @ Sat, 11 Dec 2021 13:41:50: 9000000 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 13:41:53: 5000000 INFO @ Sat, 11 Dec 2021 13:41:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.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 13:41:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:41:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:41:57: 10000000 INFO @ Sat, 11 Dec 2021 13:41:59: 6000000 INFO @ Sat, 11 Dec 2021 13:42:00: 1000000 INFO @ Sat, 11 Dec 2021 13:42:03: 11000000 INFO @ Sat, 11 Dec 2021 13:42:05: 7000000 INFO @ Sat, 11 Dec 2021 13:42:06: 2000000 INFO @ Sat, 11 Dec 2021 13:42:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:42:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:42:08: #1 total tags in treatment: 11802696 INFO @ Sat, 11 Dec 2021 13:42:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:42:08: #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 13:42:09: #1 tags after filtering in treatment: 11802696 INFO @ Sat, 11 Dec 2021 13:42:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:42:09: #1 finished! INFO @ Sat, 11 Dec 2021 13:42:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:42:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:42:10: #2 number of paired peaks: 3555 INFO @ Sat, 11 Dec 2021 13:42:10: start model_add_line... INFO @ Sat, 11 Dec 2021 13:42:10: start X-correlation... INFO @ Sat, 11 Dec 2021 13:42:10: end of X-cor INFO @ Sat, 11 Dec 2021 13:42:10: #2 finished! INFO @ Sat, 11 Dec 2021 13:42:10: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Dec 2021 13:42:10: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 11 Dec 2021 13:42:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.05_model.r WARNING @ Sat, 11 Dec 2021 13:42:10: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:42:10: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 11 Dec 2021 13:42:10: #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 13:42:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:42:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:42:10: 8000000 INFO @ Sat, 11 Dec 2021 13:42:11: 3000000 INFO @ Sat, 11 Dec 2021 13:42:16: 9000000 INFO @ Sat, 11 Dec 2021 13:42:17: 4000000 INFO @ Sat, 11 Dec 2021 13:42:22: 10000000 INFO @ Sat, 11 Dec 2021 13:42:23: 5000000 INFO @ Sat, 11 Dec 2021 13:42:27: 11000000 INFO @ Sat, 11 Dec 2021 13:42:28: 6000000 INFO @ Sat, 11 Dec 2021 13:42:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:42:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:42:32: #1 total tags in treatment: 11802696 INFO @ Sat, 11 Dec 2021 13:42:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:42:32: #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 13:42:32: #1 tags after filtering in treatment: 11802696 INFO @ Sat, 11 Dec 2021 13:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:42:32: #1 finished! INFO @ Sat, 11 Dec 2021 13:42:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:42:33: #2 number of paired peaks: 3555 INFO @ Sat, 11 Dec 2021 13:42:33: start model_add_line... INFO @ Sat, 11 Dec 2021 13:42:33: start X-correlation... INFO @ Sat, 11 Dec 2021 13:42:33: end of X-cor INFO @ Sat, 11 Dec 2021 13:42:33: #2 finished! INFO @ Sat, 11 Dec 2021 13:42:33: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Dec 2021 13:42:33: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 11 Dec 2021 13:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.10_model.r WARNING @ Sat, 11 Dec 2021 13:42:33: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:42:33: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 11 Dec 2021 13:42:33: #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 13:42:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:42:34: 7000000 INFO @ Sat, 11 Dec 2021 13:42:39: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:42:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:42:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:42:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.05_summits.bed INFO @ Sat, 11 Dec 2021 13:42:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12458 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:42:45: 9000000 INFO @ Sat, 11 Dec 2021 13:42:50: 10000000 INFO @ Sat, 11 Dec 2021 13:42:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:56: 11000000 INFO @ Sat, 11 Dec 2021 13:43:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:43:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:43:00: #1 total tags in treatment: 11802696 INFO @ Sat, 11 Dec 2021 13:43:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:43:00: #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 13:43:00: #1 tags after filtering in treatment: 11802696 INFO @ Sat, 11 Dec 2021 13:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:43:00: #1 finished! INFO @ Sat, 11 Dec 2021 13:43:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:43:01: #2 number of paired peaks: 3555 INFO @ Sat, 11 Dec 2021 13:43:01: start model_add_line... INFO @ Sat, 11 Dec 2021 13:43:01: start X-correlation... INFO @ Sat, 11 Dec 2021 13:43:01: end of X-cor INFO @ Sat, 11 Dec 2021 13:43:01: #2 finished! INFO @ Sat, 11 Dec 2021 13:43:01: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Dec 2021 13:43:01: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 11 Dec 2021 13:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.20_model.r WARNING @ Sat, 11 Dec 2021 13:43:01: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:43:01: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 11 Dec 2021 13:43:01: #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 13:43:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:43:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:43:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.10_summits.bed INFO @ Sat, 11 Dec 2021 13:43:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5821 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:43:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:43:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:43:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:43:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427705/SRX9427705.20_summits.bed INFO @ Sat, 11 Dec 2021 13:43:35: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1592 records, 4 fields): 3 millis CompletedMACS2peakCalling