Job ID = 6498617 SRX = SRX645126 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:54:54 prefetch.2.10.7: 1) Downloading 'SRR1505726'... 2020-06-26T00:54:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:58:21 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:58:21 prefetch.2.10.7: 1) 'SRR1505726' was downloaded successfully Read 17096439 spots for SRR1505726/SRR1505726.sra Written 17096439 spots for SRR1505726/SRR1505726.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:26 17096439 reads; of these: 17096439 (100.00%) were unpaired; of these: 7472313 (43.71%) aligned 0 times 8179467 (47.84%) aligned exactly 1 time 1444659 (8.45%) aligned >1 times 56.29% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 2879435 / 9624126 = 0.2992 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 @ Fri, 26 Jun 2020 10:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.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 @ Fri, 26 Jun 2020 10:11:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:11:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:12:07: 1000000 INFO @ Fri, 26 Jun 2020 10:12:18: 2000000 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 @ Fri, 26 Jun 2020 10:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.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 @ Fri, 26 Jun 2020 10:12:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:12:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:12:29: 3000000 INFO @ Fri, 26 Jun 2020 10:12:37: 1000000 INFO @ Fri, 26 Jun 2020 10:12:40: 4000000 INFO @ Fri, 26 Jun 2020 10:12:48: 2000000 INFO @ Fri, 26 Jun 2020 10:12:51: 5000000 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 @ Fri, 26 Jun 2020 10:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.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 @ Fri, 26 Jun 2020 10:12:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:12:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:12:59: 3000000 INFO @ Fri, 26 Jun 2020 10:13:03: 6000000 INFO @ Fri, 26 Jun 2020 10:13:05: 1000000 INFO @ Fri, 26 Jun 2020 10:13:11: 4000000 INFO @ Fri, 26 Jun 2020 10:13:11: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 10:13:11: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 10:13:11: #1 total tags in treatment: 6744691 INFO @ Fri, 26 Jun 2020 10:13:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:13:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:13:11: #1 tags after filtering in treatment: 6744691 INFO @ Fri, 26 Jun 2020 10:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:13:11: #1 finished! INFO @ Fri, 26 Jun 2020 10:13:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:13:12: #2 number of paired peaks: 3853 INFO @ Fri, 26 Jun 2020 10:13:12: start model_add_line... INFO @ Fri, 26 Jun 2020 10:13:12: start X-correlation... INFO @ Fri, 26 Jun 2020 10:13:12: end of X-cor INFO @ Fri, 26 Jun 2020 10:13:12: #2 finished! INFO @ Fri, 26 Jun 2020 10:13:12: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 10:13:12: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 10:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.05_model.r WARNING @ Fri, 26 Jun 2020 10:13:12: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:13:12: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Fri, 26 Jun 2020 10:13:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 10:13:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:13:14: 2000000 INFO @ Fri, 26 Jun 2020 10:13:22: 5000000 INFO @ Fri, 26 Jun 2020 10:13:23: 3000000 INFO @ Fri, 26 Jun 2020 10:13:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:13:32: 4000000 INFO @ Fri, 26 Jun 2020 10:13:34: 6000000 INFO @ Fri, 26 Jun 2020 10:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.05_summits.bed INFO @ Fri, 26 Jun 2020 10:13:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5931 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:13:41: 5000000 INFO @ Fri, 26 Jun 2020 10:13:42: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 10:13:42: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 10:13:42: #1 total tags in treatment: 6744691 INFO @ Fri, 26 Jun 2020 10:13:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:13:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:13:42: #1 tags after filtering in treatment: 6744691 INFO @ Fri, 26 Jun 2020 10:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:13:42: #1 finished! INFO @ Fri, 26 Jun 2020 10:13:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:13:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:13:43: #2 number of paired peaks: 3853 INFO @ Fri, 26 Jun 2020 10:13:43: start model_add_line... INFO @ Fri, 26 Jun 2020 10:13:43: start X-correlation... INFO @ Fri, 26 Jun 2020 10:13:43: end of X-cor INFO @ Fri, 26 Jun 2020 10:13:43: #2 finished! INFO @ Fri, 26 Jun 2020 10:13:43: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 10:13:43: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 10:13:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.10_model.r WARNING @ Fri, 26 Jun 2020 10:13:43: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:13:43: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Fri, 26 Jun 2020 10:13:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 10:13:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:13:43: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:13:50: 6000000 INFO @ Fri, 26 Jun 2020 10:13:56: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 10:13:56: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 10:13:56: #1 total tags in treatment: 6744691 INFO @ Fri, 26 Jun 2020 10:13:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:13:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 10:13:56: #1 tags after filtering in treatment: 6744691 INFO @ Fri, 26 Jun 2020 10:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:13:56: #1 finished! INFO @ Fri, 26 Jun 2020 10:13:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:13:57: #2 number of paired peaks: 3853 INFO @ Fri, 26 Jun 2020 10:13:57: start model_add_line... INFO @ Fri, 26 Jun 2020 10:13:57: start X-correlation... INFO @ Fri, 26 Jun 2020 10:13:57: end of X-cor INFO @ Fri, 26 Jun 2020 10:13:57: #2 finished! INFO @ Fri, 26 Jun 2020 10:13:57: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 10:13:57: #2 alternative fragment length(s) may be 135 bps INFO @ Fri, 26 Jun 2020 10:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.20_model.r WARNING @ Fri, 26 Jun 2020 10:13:57: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:13:57: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Fri, 26 Jun 2020 10:13:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 10:13:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:13:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.10_summits.bed INFO @ Fri, 26 Jun 2020 10:14:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4924 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:14:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:14:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:14:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:14:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645126/SRX645126.20_summits.bed INFO @ Fri, 26 Jun 2020 10:14:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3711 records, 4 fields): 6 millis CompletedMACS2peakCalling