Job ID = 14170709 SRX = SRX10000640 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 39924978 spots for SRR13606572/SRR13606572.sra Written 39924978 spots for SRR13606572/SRR13606572.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171154 ("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: 00:04:53 39924978 reads; of these: 39924978 (100.00%) were unpaired; of these: 38630813 (96.76%) aligned 0 times 823662 (2.06%) aligned exactly 1 time 470503 (1.18%) aligned >1 times 3.24% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 281911 / 1294165 = 0.2178 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 08:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.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 08:15:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:15:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:15:27: 1000000 INFO @ Sat, 11 Dec 2021 08:15:27: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 08:15:27: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 08:15:27: #1 total tags in treatment: 1012254 INFO @ Sat, 11 Dec 2021 08:15:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:15:27: #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 08:15:27: #1 tags after filtering in treatment: 1012254 INFO @ Sat, 11 Dec 2021 08:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:15:27: #1 finished! INFO @ Sat, 11 Dec 2021 08:15:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:15:27: #2 number of paired peaks: 2106 INFO @ Sat, 11 Dec 2021 08:15:27: start model_add_line... INFO @ Sat, 11 Dec 2021 08:15:27: start X-correlation... INFO @ Sat, 11 Dec 2021 08:15:27: end of X-cor INFO @ Sat, 11 Dec 2021 08:15:27: #2 finished! INFO @ Sat, 11 Dec 2021 08:15:27: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 08:15:27: #2 alternative fragment length(s) may be 51,249,561 bps INFO @ Sat, 11 Dec 2021 08:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.05_model.r WARNING @ Sat, 11 Dec 2021 08:15:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:15:27: #2 You may need to consider one of the other alternative d(s): 51,249,561 WARNING @ Sat, 11 Dec 2021 08:15:27: #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 08:15:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:15:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:15:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:15:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:15:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.05_summits.bed INFO @ Sat, 11 Dec 2021 08:15:34: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 180 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 08:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.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 08:15:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:15:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:15:58: 1000000 INFO @ Sat, 11 Dec 2021 08:15:58: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 08:15:58: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 08:15:58: #1 total tags in treatment: 1012254 INFO @ Sat, 11 Dec 2021 08:15:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:15:58: #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 08:15:58: #1 tags after filtering in treatment: 1012254 INFO @ Sat, 11 Dec 2021 08:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:15:58: #1 finished! INFO @ Sat, 11 Dec 2021 08:15:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:15:58: #2 number of paired peaks: 2106 INFO @ Sat, 11 Dec 2021 08:15:58: start model_add_line... INFO @ Sat, 11 Dec 2021 08:15:58: start X-correlation... INFO @ Sat, 11 Dec 2021 08:15:58: end of X-cor INFO @ Sat, 11 Dec 2021 08:15:58: #2 finished! INFO @ Sat, 11 Dec 2021 08:15:58: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 08:15:58: #2 alternative fragment length(s) may be 51,249,561 bps INFO @ Sat, 11 Dec 2021 08:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.10_model.r WARNING @ Sat, 11 Dec 2021 08:15:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:15:59: #2 You may need to consider one of the other alternative d(s): 51,249,561 WARNING @ Sat, 11 Dec 2021 08:15:59: #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 08:15:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:15:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:16:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.10_summits.bed INFO @ Sat, 11 Dec 2021 08:16:06: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (415 records, 4 fields): 445 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 08:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.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 08:16:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:16:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:16:28: 1000000 INFO @ Sat, 11 Dec 2021 08:16:28: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 08:16:28: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 08:16:28: #1 total tags in treatment: 1012254 INFO @ Sat, 11 Dec 2021 08:16:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:16:28: #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 08:16:28: #1 tags after filtering in treatment: 1012254 INFO @ Sat, 11 Dec 2021 08:16:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:16:28: #1 finished! INFO @ Sat, 11 Dec 2021 08:16:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:16:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:16:29: #2 number of paired peaks: 2106 INFO @ Sat, 11 Dec 2021 08:16:29: start model_add_line... INFO @ Sat, 11 Dec 2021 08:16:29: start X-correlation... INFO @ Sat, 11 Dec 2021 08:16:29: end of X-cor INFO @ Sat, 11 Dec 2021 08:16:29: #2 finished! INFO @ Sat, 11 Dec 2021 08:16:29: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 08:16:29: #2 alternative fragment length(s) may be 51,249,561 bps INFO @ Sat, 11 Dec 2021 08:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.20_model.r WARNING @ Sat, 11 Dec 2021 08:16:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:16:29: #2 You may need to consider one of the other alternative d(s): 51,249,561 WARNING @ Sat, 11 Dec 2021 08:16:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:16:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:16:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:16:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:16:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:16:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:16:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000640/SRX10000640.20_summits.bed INFO @ Sat, 11 Dec 2021 08:16:35: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling