Job ID = 14167419 SRX = ERX3978905 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29124827 spots for ERR3975974/ERR3975974.sra Written 29124827 spots for ERR3975974/ERR3975974.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168472 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:46:43 29124827 reads; of these: 29124827 (100.00%) were paired; of these: 8380595 (28.77%) aligned concordantly 0 times 15763557 (54.12%) aligned concordantly exactly 1 time 4980675 (17.10%) aligned concordantly >1 times ---- 8380595 pairs aligned concordantly 0 times; of these: 810458 (9.67%) aligned discordantly 1 time ---- 7570137 pairs aligned 0 times concordantly or discordantly; of these: 15140274 mates make up the pairs; of these: 7268227 (48.01%) aligned 0 times 4569423 (30.18%) aligned exactly 1 time 3302624 (21.81%) aligned >1 times 87.52% overall alignment rate Time searching: 01:46:44 Overall time: 01:46:44 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 24 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] 17260598 / 21282495 = 0.8110 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 14:16:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.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 14:16:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:16:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:16:12: 1000000 INFO @ Fri, 10 Dec 2021 14:16:19: 2000000 INFO @ Fri, 10 Dec 2021 14:16:26: 3000000 INFO @ Fri, 10 Dec 2021 14:16:32: 4000000 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 14:16:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.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 14:16:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:16:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:16:40: 5000000 INFO @ Fri, 10 Dec 2021 14:16:42: 1000000 INFO @ Fri, 10 Dec 2021 14:16:47: 6000000 INFO @ Fri, 10 Dec 2021 14:16:48: 2000000 INFO @ Fri, 10 Dec 2021 14:16:54: 7000000 INFO @ Fri, 10 Dec 2021 14:16:55: 3000000 INFO @ Fri, 10 Dec 2021 14:17:01: 4000000 INFO @ Fri, 10 Dec 2021 14:17:02: 8000000 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 14:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.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 14:17:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:17:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:17:08: 5000000 INFO @ Fri, 10 Dec 2021 14:17:09: 9000000 INFO @ Fri, 10 Dec 2021 14:17:12: 1000000 INFO @ Fri, 10 Dec 2021 14:17:14: 6000000 INFO @ Fri, 10 Dec 2021 14:17:17: 10000000 INFO @ Fri, 10 Dec 2021 14:17:18: 2000000 INFO @ Fri, 10 Dec 2021 14:17:21: 7000000 INFO @ Fri, 10 Dec 2021 14:17:24: 11000000 INFO @ Fri, 10 Dec 2021 14:17:25: 3000000 INFO @ Fri, 10 Dec 2021 14:17:27: 8000000 INFO @ Fri, 10 Dec 2021 14:17:31: 4000000 INFO @ Fri, 10 Dec 2021 14:17:32: 12000000 INFO @ Fri, 10 Dec 2021 14:17:34: 9000000 INFO @ Fri, 10 Dec 2021 14:17:38: 5000000 INFO @ Fri, 10 Dec 2021 14:17:40: 13000000 INFO @ Fri, 10 Dec 2021 14:17:40: 10000000 INFO @ Fri, 10 Dec 2021 14:17:44: 6000000 INFO @ Fri, 10 Dec 2021 14:17:48: 11000000 INFO @ Fri, 10 Dec 2021 14:17:48: 14000000 INFO @ Fri, 10 Dec 2021 14:17:51: 7000000 INFO @ Fri, 10 Dec 2021 14:17:54: 12000000 INFO @ Fri, 10 Dec 2021 14:17:56: 15000000 INFO @ Fri, 10 Dec 2021 14:17:57: 8000000 INFO @ Fri, 10 Dec 2021 14:18:01: 13000000 INFO @ Fri, 10 Dec 2021 14:18:03: 16000000 INFO @ Fri, 10 Dec 2021 14:18:04: 9000000 INFO @ Fri, 10 Dec 2021 14:18:06: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 14:18:06: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 14:18:06: #1 total tags in treatment: 4008758 INFO @ Fri, 10 Dec 2021 14:18:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:18:06: #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 14:18:07: #1 tags after filtering in treatment: 3391421 INFO @ Fri, 10 Dec 2021 14:18:07: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 14:18:07: #1 finished! INFO @ Fri, 10 Dec 2021 14:18:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:18:07: #2 number of paired peaks: 4177 INFO @ Fri, 10 Dec 2021 14:18:07: start model_add_line... INFO @ Fri, 10 Dec 2021 14:18:07: start X-correlation... INFO @ Fri, 10 Dec 2021 14:18:07: end of X-cor INFO @ Fri, 10 Dec 2021 14:18:07: #2 finished! INFO @ Fri, 10 Dec 2021 14:18:07: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 14:18:07: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 14:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.05_model.r WARNING @ Fri, 10 Dec 2021 14:18:07: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:18:07: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Fri, 10 Dec 2021 14:18:07: #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 14:18:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:18:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:18:08: 14000000 INFO @ Fri, 10 Dec 2021 14:18:11: 10000000 INFO @ Fri, 10 Dec 2021 14:18:15: 15000000 INFO @ Fri, 10 Dec 2021 14:18:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:18:17: 11000000 INFO @ Fri, 10 Dec 2021 14:18:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:18:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:18:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.05_summits.bed INFO @ Fri, 10 Dec 2021 14:18:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9188 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:18:21: 16000000 INFO @ Fri, 10 Dec 2021 14:18:24: 12000000 INFO @ Fri, 10 Dec 2021 14:18:24: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 14:18:24: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 14:18:24: #1 total tags in treatment: 4008758 INFO @ Fri, 10 Dec 2021 14:18:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:18:24: #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 14:18:24: #1 tags after filtering in treatment: 3391421 INFO @ Fri, 10 Dec 2021 14:18:24: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 14:18:24: #1 finished! INFO @ Fri, 10 Dec 2021 14:18:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:18:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:18:24: #2 number of paired peaks: 4177 INFO @ Fri, 10 Dec 2021 14:18:24: start model_add_line... INFO @ Fri, 10 Dec 2021 14:18:24: start X-correlation... INFO @ Fri, 10 Dec 2021 14:18:24: end of X-cor INFO @ Fri, 10 Dec 2021 14:18:24: #2 finished! INFO @ Fri, 10 Dec 2021 14:18:24: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 14:18:24: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 14:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.10_model.r WARNING @ Fri, 10 Dec 2021 14:18:24: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:18:24: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Fri, 10 Dec 2021 14:18:24: #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 14:18:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:18:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:18:30: 13000000 INFO @ Fri, 10 Dec 2021 14:18:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:18:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:18:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:18:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.10_summits.bed INFO @ Fri, 10 Dec 2021 14:18:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5332 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:18:36: 14000000 INFO @ Fri, 10 Dec 2021 14:18:42: 15000000 INFO @ Fri, 10 Dec 2021 14:18:48: 16000000 INFO @ Fri, 10 Dec 2021 14:18:51: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 14:18:51: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 14:18:51: #1 total tags in treatment: 4008758 INFO @ Fri, 10 Dec 2021 14:18:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:18:51: #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 14:18:51: #1 tags after filtering in treatment: 3391421 INFO @ Fri, 10 Dec 2021 14:18:51: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 14:18:51: #1 finished! INFO @ Fri, 10 Dec 2021 14:18:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:18:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:18:52: #2 number of paired peaks: 4177 INFO @ Fri, 10 Dec 2021 14:18:52: start model_add_line... INFO @ Fri, 10 Dec 2021 14:18:52: start X-correlation... INFO @ Fri, 10 Dec 2021 14:18:52: end of X-cor INFO @ Fri, 10 Dec 2021 14:18:52: #2 finished! INFO @ Fri, 10 Dec 2021 14:18:52: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 14:18:52: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 14:18:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.20_model.r WARNING @ Fri, 10 Dec 2021 14:18:52: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:18:52: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Fri, 10 Dec 2021 14:18:52: #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 14:18:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:18:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:19:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:19:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:19:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978905/ERX3978905.20_summits.bed INFO @ Fri, 10 Dec 2021 14:19:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1769 records, 4 fields): 3 millis CompletedMACS2peakCalling