Job ID = 14168700 SRX = ERX3978763 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18672518 spots for ERR3975778/ERR3975778.sra Written 18672518 spots for ERR3975778/ERR3975778.sra Read 18774743 spots for ERR3975794/ERR3975794.sra Written 18774743 spots for ERR3975794/ERR3975794.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169854 ("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: 00:59:15 37447261 reads; of these: 37447261 (100.00%) were paired; of these: 12168372 (32.49%) aligned concordantly 0 times 2855672 (7.63%) aligned concordantly exactly 1 time 22423217 (59.88%) aligned concordantly >1 times ---- 12168372 pairs aligned concordantly 0 times; of these: 1035457 (8.51%) aligned discordantly 1 time ---- 11132915 pairs aligned 0 times concordantly or discordantly; of these: 22265830 mates make up the pairs; of these: 9704096 (43.58%) aligned 0 times 374575 (1.68%) aligned exactly 1 time 12187159 (54.73%) aligned >1 times 87.04% overall alignment rate Time searching: 00:59:15 Overall time: 00:59:15 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 48 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] 19968829 / 26072529 = 0.7659 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 20:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.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 20:46:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:46:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:46:07: 1000000 INFO @ Fri, 10 Dec 2021 20:46:13: 2000000 INFO @ Fri, 10 Dec 2021 20:46:19: 3000000 INFO @ Fri, 10 Dec 2021 20:46:24: 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 20:46:30: 5000000 INFO @ Fri, 10 Dec 2021 20:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.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 20:46:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:46:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:46:36: 6000000 INFO @ Fri, 10 Dec 2021 20:46:37: 1000000 INFO @ Fri, 10 Dec 2021 20:46:41: 7000000 INFO @ Fri, 10 Dec 2021 20:46:43: 2000000 INFO @ Fri, 10 Dec 2021 20:46:47: 8000000 INFO @ Fri, 10 Dec 2021 20:46:49: 3000000 INFO @ Fri, 10 Dec 2021 20:46:52: 9000000 INFO @ Fri, 10 Dec 2021 20:46:55: 4000000 INFO @ Fri, 10 Dec 2021 20:46:57: 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 20:47:00: 5000000 INFO @ Fri, 10 Dec 2021 20:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.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 20:47:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:47:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:47:02: 11000000 INFO @ Fri, 10 Dec 2021 20:47:07: 6000000 INFO @ Fri, 10 Dec 2021 20:47:08: 12000000 INFO @ Fri, 10 Dec 2021 20:47:09: 1000000 INFO @ Fri, 10 Dec 2021 20:47:12: 7000000 INFO @ Fri, 10 Dec 2021 20:47:13: 13000000 INFO @ Fri, 10 Dec 2021 20:47:16: 2000000 INFO @ Fri, 10 Dec 2021 20:47:18: 8000000 INFO @ Fri, 10 Dec 2021 20:47:19: 14000000 INFO @ Fri, 10 Dec 2021 20:47:23: 9000000 INFO @ Fri, 10 Dec 2021 20:47:24: 3000000 INFO @ Fri, 10 Dec 2021 20:47:25: 15000000 INFO @ Fri, 10 Dec 2021 20:47:29: 10000000 INFO @ Fri, 10 Dec 2021 20:47:30: 16000000 INFO @ Fri, 10 Dec 2021 20:47:31: 4000000 INFO @ Fri, 10 Dec 2021 20:47:34: 11000000 INFO @ Fri, 10 Dec 2021 20:47:36: 17000000 INFO @ Fri, 10 Dec 2021 20:47:39: 5000000 INFO @ Fri, 10 Dec 2021 20:47:40: 12000000 INFO @ Fri, 10 Dec 2021 20:47:41: 18000000 INFO @ Fri, 10 Dec 2021 20:47:45: 13000000 INFO @ Fri, 10 Dec 2021 20:47:46: 6000000 INFO @ Fri, 10 Dec 2021 20:47:47: 19000000 INFO @ Fri, 10 Dec 2021 20:47:51: 14000000 INFO @ Fri, 10 Dec 2021 20:47:52: 20000000 INFO @ Fri, 10 Dec 2021 20:47:54: 7000000 INFO @ Fri, 10 Dec 2021 20:47:56: 15000000 INFO @ Fri, 10 Dec 2021 20:47:58: 21000000 INFO @ Fri, 10 Dec 2021 20:48:01: 8000000 INFO @ Fri, 10 Dec 2021 20:48:02: 16000000 INFO @ Fri, 10 Dec 2021 20:48:03: 22000000 INFO @ Fri, 10 Dec 2021 20:48:07: 17000000 INFO @ Fri, 10 Dec 2021 20:48:07: 9000000 INFO @ Fri, 10 Dec 2021 20:48:09: 23000000 INFO @ Fri, 10 Dec 2021 20:48:13: 18000000 INFO @ Fri, 10 Dec 2021 20:48:14: 10000000 INFO @ Fri, 10 Dec 2021 20:48:15: 24000000 INFO @ Fri, 10 Dec 2021 20:48:18: 19000000 INFO @ Fri, 10 Dec 2021 20:48:21: 25000000 INFO @ Fri, 10 Dec 2021 20:48:21: 11000000 INFO @ Fri, 10 Dec 2021 20:48:22: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:48:22: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:48:22: #1 total tags in treatment: 5449422 INFO @ Fri, 10 Dec 2021 20:48:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:48:22: #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 20:48:22: #1 tags after filtering in treatment: 3035357 INFO @ Fri, 10 Dec 2021 20:48:22: #1 Redundant rate of treatment: 0.44 INFO @ Fri, 10 Dec 2021 20:48:22: #1 finished! INFO @ Fri, 10 Dec 2021 20:48:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:48:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:48:23: #2 number of paired peaks: 4268 INFO @ Fri, 10 Dec 2021 20:48:23: start model_add_line... INFO @ Fri, 10 Dec 2021 20:48:23: start X-correlation... INFO @ Fri, 10 Dec 2021 20:48:23: end of X-cor INFO @ Fri, 10 Dec 2021 20:48:23: #2 finished! INFO @ Fri, 10 Dec 2021 20:48:23: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 20:48:23: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 20:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.05_model.r WARNING @ Fri, 10 Dec 2021 20:48:23: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:48:23: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Fri, 10 Dec 2021 20:48:23: #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 20:48:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:48:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:48:24: 20000000 INFO @ Fri, 10 Dec 2021 20:48:28: 12000000 INFO @ Fri, 10 Dec 2021 20:48:30: 21000000 INFO @ Fri, 10 Dec 2021 20:48:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.05_summits.bed INFO @ Fri, 10 Dec 2021 20:48:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7074 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:48:35: 13000000 INFO @ Fri, 10 Dec 2021 20:48:35: 22000000 INFO @ Fri, 10 Dec 2021 20:48:41: 23000000 INFO @ Fri, 10 Dec 2021 20:48:42: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:48:47: 24000000 INFO @ Fri, 10 Dec 2021 20:48:49: 15000000 INFO @ Fri, 10 Dec 2021 20:48:53: 25000000 INFO @ Fri, 10 Dec 2021 20:48:54: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:48:54: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:48:54: #1 total tags in treatment: 5449422 INFO @ Fri, 10 Dec 2021 20:48:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:48:54: #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 20:48:55: #1 tags after filtering in treatment: 3035357 INFO @ Fri, 10 Dec 2021 20:48:55: #1 Redundant rate of treatment: 0.44 INFO @ Fri, 10 Dec 2021 20:48:55: #1 finished! INFO @ Fri, 10 Dec 2021 20:48:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:48:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:48:55: #2 number of paired peaks: 4268 INFO @ Fri, 10 Dec 2021 20:48:55: start model_add_line... INFO @ Fri, 10 Dec 2021 20:48:55: start X-correlation... INFO @ Fri, 10 Dec 2021 20:48:55: end of X-cor INFO @ Fri, 10 Dec 2021 20:48:55: #2 finished! INFO @ Fri, 10 Dec 2021 20:48:55: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 20:48:55: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 20:48:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.10_model.r WARNING @ Fri, 10 Dec 2021 20:48:55: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:48:55: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Fri, 10 Dec 2021 20:48:55: #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 20:48:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:48:56: 16000000 INFO @ Fri, 10 Dec 2021 20:49:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:49:03: 17000000 INFO @ Fri, 10 Dec 2021 20:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.10_summits.bed INFO @ Fri, 10 Dec 2021 20:49:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3776 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:49:09: 18000000 INFO @ Fri, 10 Dec 2021 20:49:16: 19000000 INFO @ Fri, 10 Dec 2021 20:49:23: 20000000 INFO @ Fri, 10 Dec 2021 20:49:30: 21000000 INFO @ Fri, 10 Dec 2021 20:49:36: 22000000 INFO @ Fri, 10 Dec 2021 20:49:43: 23000000 INFO @ Fri, 10 Dec 2021 20:49:50: 24000000 INFO @ Fri, 10 Dec 2021 20:49:58: 25000000 INFO @ Fri, 10 Dec 2021 20:49:59: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:49:59: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:49:59: #1 total tags in treatment: 5449422 INFO @ Fri, 10 Dec 2021 20:49:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:49:59: #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 20:49:59: #1 tags after filtering in treatment: 3035357 INFO @ Fri, 10 Dec 2021 20:49:59: #1 Redundant rate of treatment: 0.44 INFO @ Fri, 10 Dec 2021 20:49:59: #1 finished! INFO @ Fri, 10 Dec 2021 20:49:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:50:00: #2 number of paired peaks: 4268 INFO @ Fri, 10 Dec 2021 20:50:00: start model_add_line... INFO @ Fri, 10 Dec 2021 20:50:00: start X-correlation... INFO @ Fri, 10 Dec 2021 20:50:00: end of X-cor INFO @ Fri, 10 Dec 2021 20:50:00: #2 finished! INFO @ Fri, 10 Dec 2021 20:50:00: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Dec 2021 20:50:00: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Dec 2021 20:50:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.20_model.r WARNING @ Fri, 10 Dec 2021 20:50:00: #2 Since the d (212) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:50:00: #2 You may need to consider one of the other alternative d(s): 212 WARNING @ Fri, 10 Dec 2021 20:50:00: #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 20:50:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:50:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:50:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978763/ERX3978763.20_summits.bed INFO @ Fri, 10 Dec 2021 20:50:11: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1236 records, 4 fields): 3 millis CompletedMACS2peakCalling