Job ID = 14168191 SRX = ERX3978837 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21833866 spots for ERR3975906/ERR3975906.sra Written 21833866 spots for ERR3975906/ERR3975906.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169301 ("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: 01:14:13 21833866 reads; of these: 21833866 (100.00%) were paired; of these: 7582101 (34.73%) aligned concordantly 0 times 10796773 (49.45%) aligned concordantly exactly 1 time 3454992 (15.82%) aligned concordantly >1 times ---- 7582101 pairs aligned concordantly 0 times; of these: 595028 (7.85%) aligned discordantly 1 time ---- 6987073 pairs aligned 0 times concordantly or discordantly; of these: 13974146 mates make up the pairs; of these: 6954754 (49.77%) aligned 0 times 4209118 (30.12%) aligned exactly 1 time 2810274 (20.11%) aligned >1 times 84.07% overall alignment rate Time searching: 01:14:13 Overall time: 01:14:13 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 16 files... [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] 10835748 / 14664180 = 0.7389 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 @ Fri, 10 Dec 2021 17:26:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.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, 10 Dec 2021 17:26:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:26:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:26:28: 1000000 INFO @ Fri, 10 Dec 2021 17:26:34: 2000000 INFO @ Fri, 10 Dec 2021 17:26:39: 3000000 INFO @ Fri, 10 Dec 2021 17:26:44: 4000000 INFO @ Fri, 10 Dec 2021 17:26:49: 5000000 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 @ Fri, 10 Dec 2021 17:26:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.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, 10 Dec 2021 17:26:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:26:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:26:55: 6000000 INFO @ Fri, 10 Dec 2021 17:27:01: 1000000 INFO @ Fri, 10 Dec 2021 17:27:01: 7000000 INFO @ Fri, 10 Dec 2021 17:27:08: 8000000 INFO @ Fri, 10 Dec 2021 17:27:08: 2000000 INFO @ Fri, 10 Dec 2021 17:27:14: 9000000 INFO @ Fri, 10 Dec 2021 17:27:16: 3000000 INFO @ Fri, 10 Dec 2021 17:27:21: 10000000 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 @ Fri, 10 Dec 2021 17:27:24: 4000000 INFO @ Fri, 10 Dec 2021 17:27:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.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, 10 Dec 2021 17:27:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:27:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:27:27: 11000000 INFO @ Fri, 10 Dec 2021 17:27:31: 1000000 INFO @ Fri, 10 Dec 2021 17:27:31: 5000000 INFO @ Fri, 10 Dec 2021 17:27:34: 12000000 INFO @ Fri, 10 Dec 2021 17:27:37: 2000000 INFO @ Fri, 10 Dec 2021 17:27:39: 6000000 INFO @ Fri, 10 Dec 2021 17:27:41: 13000000 INFO @ Fri, 10 Dec 2021 17:27:44: 3000000 INFO @ Fri, 10 Dec 2021 17:27:47: 7000000 INFO @ Fri, 10 Dec 2021 17:27:47: 14000000 INFO @ Fri, 10 Dec 2021 17:27:51: 4000000 INFO @ Fri, 10 Dec 2021 17:27:54: 15000000 INFO @ Fri, 10 Dec 2021 17:27:54: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:27:54: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:27:54: #1 total tags in treatment: 3774991 INFO @ Fri, 10 Dec 2021 17:27:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:27:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:27:54: 8000000 INFO @ Fri, 10 Dec 2021 17:27:54: #1 tags after filtering in treatment: 3473896 INFO @ Fri, 10 Dec 2021 17:27:54: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:27:54: #1 finished! INFO @ Fri, 10 Dec 2021 17:27:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:27:55: #2 number of paired peaks: 1932 INFO @ Fri, 10 Dec 2021 17:27:55: start model_add_line... INFO @ Fri, 10 Dec 2021 17:27:55: start X-correlation... INFO @ Fri, 10 Dec 2021 17:27:55: end of X-cor INFO @ Fri, 10 Dec 2021 17:27:55: #2 finished! INFO @ Fri, 10 Dec 2021 17:27:55: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 17:27:55: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 17:27:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.05_model.r WARNING @ Fri, 10 Dec 2021 17:27:55: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:27:55: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 17:27:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:27:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:27:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:27:57: 5000000 INFO @ Fri, 10 Dec 2021 17:28:02: 9000000 INFO @ Fri, 10 Dec 2021 17:28:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:28:04: 6000000 INFO @ Fri, 10 Dec 2021 17:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.05_summits.bed INFO @ Fri, 10 Dec 2021 17:28:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4289 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:28:10: 10000000 INFO @ Fri, 10 Dec 2021 17:28:10: 7000000 INFO @ Fri, 10 Dec 2021 17:28:17: 8000000 INFO @ Fri, 10 Dec 2021 17:28:18: 11000000 INFO @ Fri, 10 Dec 2021 17:28:23: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:28:25: 12000000 INFO @ Fri, 10 Dec 2021 17:28:30: 10000000 INFO @ Fri, 10 Dec 2021 17:28:34: 13000000 INFO @ Fri, 10 Dec 2021 17:28:37: 11000000 INFO @ Fri, 10 Dec 2021 17:28:41: 14000000 INFO @ Fri, 10 Dec 2021 17:28:43: 12000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:28:49: 15000000 INFO @ Fri, 10 Dec 2021 17:28:49: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:28:49: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:28:49: #1 total tags in treatment: 3774991 INFO @ Fri, 10 Dec 2021 17:28:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:28:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:28:49: #1 tags after filtering in treatment: 3473896 INFO @ Fri, 10 Dec 2021 17:28:49: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:28:49: #1 finished! INFO @ Fri, 10 Dec 2021 17:28:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:28:49: #2 number of paired peaks: 1932 INFO @ Fri, 10 Dec 2021 17:28:49: start model_add_line... INFO @ Fri, 10 Dec 2021 17:28:50: start X-correlation... INFO @ Fri, 10 Dec 2021 17:28:50: end of X-cor INFO @ Fri, 10 Dec 2021 17:28:50: #2 finished! INFO @ Fri, 10 Dec 2021 17:28:50: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 17:28:50: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 17:28:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.10_model.r WARNING @ Fri, 10 Dec 2021 17:28:50: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:28:50: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 17:28:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:28:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:28:50: 13000000 INFO @ Fri, 10 Dec 2021 17:28:56: 14000000 INFO @ Fri, 10 Dec 2021 17:28:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.10_summits.bed INFO @ Fri, 10 Dec 2021 17:29:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1790 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:29:02: 15000000 INFO @ Fri, 10 Dec 2021 17:29:02: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:29:02: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:29:02: #1 total tags in treatment: 3774991 INFO @ Fri, 10 Dec 2021 17:29:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:29:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:29:02: #1 tags after filtering in treatment: 3473896 INFO @ Fri, 10 Dec 2021 17:29:02: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:29:02: #1 finished! INFO @ Fri, 10 Dec 2021 17:29:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:29:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:29:03: #2 number of paired peaks: 1932 INFO @ Fri, 10 Dec 2021 17:29:03: start model_add_line... INFO @ Fri, 10 Dec 2021 17:29:03: start X-correlation... INFO @ Fri, 10 Dec 2021 17:29:03: end of X-cor INFO @ Fri, 10 Dec 2021 17:29:03: #2 finished! INFO @ Fri, 10 Dec 2021 17:29:03: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 17:29:03: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 17:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.20_model.r WARNING @ Fri, 10 Dec 2021 17:29:03: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:29:03: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 17:29:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:29:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:29:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978837/ERX3978837.20_summits.bed INFO @ Fri, 10 Dec 2021 17:29:14: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (685 records, 4 fields): 3 millis CompletedMACS2peakCalling