Job ID = 10165845 SRX = SRX7723690 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9112030 spots for SRR11084646/SRR11084646.sra Written 9112030 spots for SRR11084646/SRR11084646.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166138 ("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: 00:03:40 9112030 reads; of these: 9112030 (100.00%) were unpaired; of these: 971010 (10.66%) aligned 0 times 5734788 (62.94%) aligned exactly 1 time 2406232 (26.41%) aligned >1 times 89.34% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 697653 / 8141020 = 0.0857 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.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 @ Thu, 08 Oct 2020 20:05:27: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:27: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:34: 1000000 INFO @ Thu, 08 Oct 2020 20:05:41: 2000000 INFO @ Thu, 08 Oct 2020 20:05:48: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:05:55: 4000000 INFO @ Thu, 08 Oct 2020 20:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.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 @ Thu, 08 Oct 2020 20:05:56: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:56: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:06:03: 5000000 INFO @ Thu, 08 Oct 2020 20:06:04: 1000000 INFO @ Thu, 08 Oct 2020 20:06:10: 6000000 INFO @ Thu, 08 Oct 2020 20:06:12: 2000000 INFO @ Thu, 08 Oct 2020 20:06:19: 7000000 INFO @ Thu, 08 Oct 2020 20:06:20: 3000000 INFO @ Thu, 08 Oct 2020 20:06:22: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:06:22: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:06:22: #1 total tags in treatment: 7443367 INFO @ Thu, 08 Oct 2020 20:06:22: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:06:22: #1 tags after filtering in treatment: 7443366 INFO @ Thu, 08 Oct 2020 20:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:22: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:22: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:23: #2 number of paired peaks: 1129 INFO @ Thu, 08 Oct 2020 20:06:23: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:23: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:23: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:23: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:23: #2 predicted fragment length is 117 bps INFO @ Thu, 08 Oct 2020 20:06:23: #2 alternative fragment length(s) may be 117 bps INFO @ Thu, 08 Oct 2020 20:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.05_model.r WARNING @ Thu, 08 Oct 2020 20:06:23: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:23: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Thu, 08 Oct 2020 20:06:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:06:23: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.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 @ Thu, 08 Oct 2020 20:06:26: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:06:26: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:06:27: 4000000 INFO @ Thu, 08 Oct 2020 20:06:34: 1000000 INFO @ Thu, 08 Oct 2020 20:06:35: 5000000 INFO @ Thu, 08 Oct 2020 20:06:39: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:42: 2000000 INFO @ Thu, 08 Oct 2020 20:06:43: 6000000 INFO @ Thu, 08 Oct 2020 20:06:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.05_summits.bed INFO @ Thu, 08 Oct 2020 20:06:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4735 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:06:51: 7000000 INFO @ Thu, 08 Oct 2020 20:06:51: 3000000 INFO @ Thu, 08 Oct 2020 20:06:54: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:06:54: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:06:54: #1 total tags in treatment: 7443367 INFO @ Thu, 08 Oct 2020 20:06:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:06:54: #1 tags after filtering in treatment: 7443366 INFO @ Thu, 08 Oct 2020 20:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:54: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:55: #2 number of paired peaks: 1129 INFO @ Thu, 08 Oct 2020 20:06:55: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:55: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:55: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:55: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:55: #2 predicted fragment length is 117 bps INFO @ Thu, 08 Oct 2020 20:06:55: #2 alternative fragment length(s) may be 117 bps INFO @ Thu, 08 Oct 2020 20:06:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.10_model.r WARNING @ Thu, 08 Oct 2020 20:06:55: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:55: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Thu, 08 Oct 2020 20:06:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:06:55: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:59: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:07:07: 5000000 INFO @ Thu, 08 Oct 2020 20:07:11: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:14: 6000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.10_summits.bed INFO @ Thu, 08 Oct 2020 20:07:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1809 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:22: 7000000 INFO @ Thu, 08 Oct 2020 20:07:25: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:07:25: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:07:25: #1 total tags in treatment: 7443367 INFO @ Thu, 08 Oct 2020 20:07:25: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:07:25: #1 tags after filtering in treatment: 7443366 INFO @ Thu, 08 Oct 2020 20:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:25: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:25: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:26: #2 number of paired peaks: 1129 INFO @ Thu, 08 Oct 2020 20:07:26: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:26: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:26: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:26: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:26: #2 predicted fragment length is 117 bps INFO @ Thu, 08 Oct 2020 20:07:26: #2 alternative fragment length(s) may be 117 bps INFO @ Thu, 08 Oct 2020 20:07:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.20_model.r WARNING @ Thu, 08 Oct 2020 20:07:26: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:07:26: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Thu, 08 Oct 2020 20:07:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:07:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:42: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723690/SRX7723690.20_summits.bed INFO @ Thu, 08 Oct 2020 20:07:51: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (655 records, 4 fields): 2 millis CompletedMACS2peakCalling