Job ID = 14170017 SRX = SRX8556348 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25793138 spots for SRR12024958/SRR12024958.sra Written 25793138 spots for SRR12024958/SRR12024958.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170630 ("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: 00:09:58 25793138 reads; of these: 25793138 (100.00%) were paired; of these: 25292288 (98.06%) aligned concordantly 0 times 375302 (1.46%) aligned concordantly exactly 1 time 125548 (0.49%) aligned concordantly >1 times ---- 25292288 pairs aligned concordantly 0 times; of these: 59859 (0.24%) aligned discordantly 1 time ---- 25232429 pairs aligned 0 times concordantly or discordantly; of these: 50464858 mates make up the pairs; of these: 50289959 (99.65%) aligned 0 times 83564 (0.17%) aligned exactly 1 time 91335 (0.18%) aligned >1 times 2.51% overall alignment rate Time searching: 00:09:58 Overall time: 00:09:58 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 357238 / 554151 = 0.6447 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 04:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.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 04:50:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:50:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:51:03: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 04:51:03: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 04:51:03: #1 total tags in treatment: 172204 INFO @ Sat, 11 Dec 2021 04:51:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:51:03: #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 04:51:03: #1 tags after filtering in treatment: 157460 INFO @ Sat, 11 Dec 2021 04:51:03: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 04:51:03: #1 finished! INFO @ Sat, 11 Dec 2021 04:51:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:51:04: #2 number of paired peaks: 2831 INFO @ Sat, 11 Dec 2021 04:51:04: start model_add_line... INFO @ Sat, 11 Dec 2021 04:51:04: start X-correlation... INFO @ Sat, 11 Dec 2021 04:51:04: end of X-cor INFO @ Sat, 11 Dec 2021 04:51:04: #2 finished! INFO @ Sat, 11 Dec 2021 04:51:04: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Dec 2021 04:51:04: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Dec 2021 04:51:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.05_model.r WARNING @ Sat, 11 Dec 2021 04:51:04: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:51:04: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sat, 11 Dec 2021 04:51:04: #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 04:51:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:51:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:51:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:51:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.05_peaks.xls INFO @ Sat, 11 Dec 2021 04:51:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:51:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.05_summits.bed INFO @ Sat, 11 Dec 2021 04:51:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (681 records, 4 fields): 3 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 04:51:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.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 04:51:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:51:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:51:34: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 04:51:34: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 04:51:34: #1 total tags in treatment: 172204 INFO @ Sat, 11 Dec 2021 04:51:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:51:34: #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 04:51:34: #1 tags after filtering in treatment: 157460 INFO @ Sat, 11 Dec 2021 04:51:34: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 04:51:34: #1 finished! INFO @ Sat, 11 Dec 2021 04:51:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:51:34: #2 number of paired peaks: 2831 INFO @ Sat, 11 Dec 2021 04:51:34: start model_add_line... INFO @ Sat, 11 Dec 2021 04:51:34: start X-correlation... INFO @ Sat, 11 Dec 2021 04:51:34: end of X-cor INFO @ Sat, 11 Dec 2021 04:51:34: #2 finished! INFO @ Sat, 11 Dec 2021 04:51:34: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Dec 2021 04:51:34: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Dec 2021 04:51:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.10_model.r WARNING @ Sat, 11 Dec 2021 04:51:34: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:51:34: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sat, 11 Dec 2021 04:51:34: #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 04:51:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:51:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:51:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.10_peaks.xls INFO @ Sat, 11 Dec 2021 04:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.10_summits.bed INFO @ Sat, 11 Dec 2021 04:51:35: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (332 records, 4 fields): 2 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 04:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.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 04:51:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:51:59: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 04:52:05: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 04:52:05: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 04:52:05: #1 total tags in treatment: 172204 INFO @ Sat, 11 Dec 2021 04:52:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:52:05: #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 04:52:05: #1 tags after filtering in treatment: 157460 INFO @ Sat, 11 Dec 2021 04:52:05: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 04:52:05: #1 finished! INFO @ Sat, 11 Dec 2021 04:52:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:52:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:52:05: #2 number of paired peaks: 2831 INFO @ Sat, 11 Dec 2021 04:52:05: start model_add_line... INFO @ Sat, 11 Dec 2021 04:52:05: start X-correlation... INFO @ Sat, 11 Dec 2021 04:52:05: end of X-cor INFO @ Sat, 11 Dec 2021 04:52:05: #2 finished! INFO @ Sat, 11 Dec 2021 04:52:05: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Dec 2021 04:52:05: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Dec 2021 04:52:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.20_model.r WARNING @ Sat, 11 Dec 2021 04:52:05: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:52:05: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sat, 11 Dec 2021 04:52:05: #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 04:52:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:52:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.20_peaks.xls INFO @ Sat, 11 Dec 2021 04:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556348/SRX8556348.20_summits.bed INFO @ Sat, 11 Dec 2021 04:52:06: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 2 millis CompletedMACS2peakCalling