Job ID = 14168420 SRX = ERX3978863 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 53391618 spots for ERR3975932/ERR3975932.sra Written 53391618 spots for ERR3975932/ERR3975932.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169945 ("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: 03:28:44 53391618 reads; of these: 53391618 (100.00%) were paired; of these: 6319840 (11.84%) aligned concordantly 0 times 36698004 (68.73%) aligned concordantly exactly 1 time 10373774 (19.43%) aligned concordantly >1 times ---- 6319840 pairs aligned concordantly 0 times; of these: 1383124 (21.89%) aligned discordantly 1 time ---- 4936716 pairs aligned 0 times concordantly or discordantly; of these: 9873432 mates make up the pairs; of these: 4865384 (49.28%) aligned 0 times 2458028 (24.90%) aligned exactly 1 time 2550020 (25.83%) aligned >1 times 95.44% overall alignment rate Time searching: 03:28:44 Overall time: 03:28:44 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 44 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] 36010786 / 48221044 = 0.7468 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 22:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.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 22:29:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:29:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:30:06: 1000000 INFO @ Fri, 10 Dec 2021 22:30:14: 2000000 INFO @ Fri, 10 Dec 2021 22:30:23: 3000000 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 22:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.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 22:30:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:30:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:30:31: 4000000 INFO @ Fri, 10 Dec 2021 22:30:35: 1000000 INFO @ Fri, 10 Dec 2021 22:30:40: 5000000 INFO @ Fri, 10 Dec 2021 22:30:44: 2000000 INFO @ Fri, 10 Dec 2021 22:30:49: 6000000 INFO @ Fri, 10 Dec 2021 22:30:53: 3000000 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 22:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.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 22:30:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:30:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:30:58: 7000000 INFO @ Fri, 10 Dec 2021 22:31:02: 4000000 INFO @ Fri, 10 Dec 2021 22:31:08: 8000000 INFO @ Fri, 10 Dec 2021 22:31:08: 1000000 INFO @ Fri, 10 Dec 2021 22:31:11: 5000000 INFO @ Fri, 10 Dec 2021 22:31:16: 9000000 INFO @ Fri, 10 Dec 2021 22:31:19: 6000000 INFO @ Fri, 10 Dec 2021 22:31:20: 2000000 INFO @ Fri, 10 Dec 2021 22:31:25: 10000000 INFO @ Fri, 10 Dec 2021 22:31:29: 7000000 INFO @ Fri, 10 Dec 2021 22:31:33: 3000000 INFO @ Fri, 10 Dec 2021 22:31:34: 11000000 INFO @ Fri, 10 Dec 2021 22:31:37: 8000000 INFO @ Fri, 10 Dec 2021 22:31:43: 12000000 INFO @ Fri, 10 Dec 2021 22:31:45: 4000000 INFO @ Fri, 10 Dec 2021 22:31:46: 9000000 INFO @ Fri, 10 Dec 2021 22:31:52: 13000000 INFO @ Fri, 10 Dec 2021 22:31:55: 10000000 INFO @ Fri, 10 Dec 2021 22:31:57: 5000000 INFO @ Fri, 10 Dec 2021 22:32:01: 14000000 INFO @ Fri, 10 Dec 2021 22:32:05: 11000000 INFO @ Fri, 10 Dec 2021 22:32:09: 6000000 INFO @ Fri, 10 Dec 2021 22:32:11: 15000000 INFO @ Fri, 10 Dec 2021 22:32:15: 12000000 INFO @ Fri, 10 Dec 2021 22:32:21: 7000000 INFO @ Fri, 10 Dec 2021 22:32:22: 16000000 INFO @ Fri, 10 Dec 2021 22:32:25: 13000000 INFO @ Fri, 10 Dec 2021 22:32:31: 17000000 INFO @ Fri, 10 Dec 2021 22:32:34: 8000000 INFO @ Fri, 10 Dec 2021 22:32:35: 14000000 INFO @ Fri, 10 Dec 2021 22:32:41: 18000000 INFO @ Fri, 10 Dec 2021 22:32:45: 15000000 INFO @ Fri, 10 Dec 2021 22:32:46: 9000000 INFO @ Fri, 10 Dec 2021 22:32:52: 19000000 INFO @ Fri, 10 Dec 2021 22:32:55: 16000000 INFO @ Fri, 10 Dec 2021 22:32:58: 10000000 INFO @ Fri, 10 Dec 2021 22:33:02: 20000000 INFO @ Fri, 10 Dec 2021 22:33:04: 17000000 INFO @ Fri, 10 Dec 2021 22:33:10: 11000000 INFO @ Fri, 10 Dec 2021 22:33:10: 21000000 INFO @ Fri, 10 Dec 2021 22:33:13: 18000000 INFO @ Fri, 10 Dec 2021 22:33:19: 22000000 INFO @ Fri, 10 Dec 2021 22:33:22: 19000000 INFO @ Fri, 10 Dec 2021 22:33:22: 12000000 INFO @ Fri, 10 Dec 2021 22:33:28: 23000000 INFO @ Fri, 10 Dec 2021 22:33:31: 20000000 INFO @ Fri, 10 Dec 2021 22:33:34: 13000000 INFO @ Fri, 10 Dec 2021 22:33:37: 24000000 INFO @ Fri, 10 Dec 2021 22:33:40: 21000000 INFO @ Fri, 10 Dec 2021 22:33:46: 25000000 INFO @ Fri, 10 Dec 2021 22:33:47: 14000000 INFO @ Fri, 10 Dec 2021 22:33:50: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:33:55: 26000000 INFO @ Fri, 10 Dec 2021 22:33:59: 23000000 INFO @ Fri, 10 Dec 2021 22:34:00: 15000000 INFO @ Fri, 10 Dec 2021 22:34:04: 27000000 INFO @ Fri, 10 Dec 2021 22:34:08: 24000000 INFO @ Fri, 10 Dec 2021 22:34:12: 16000000 INFO @ Fri, 10 Dec 2021 22:34:13: 28000000 INFO @ Fri, 10 Dec 2021 22:34:17: 25000000 INFO @ Fri, 10 Dec 2021 22:34:22: 29000000 INFO @ Fri, 10 Dec 2021 22:34:24: 17000000 INFO @ Fri, 10 Dec 2021 22:34:26: 26000000 INFO @ Fri, 10 Dec 2021 22:34:29: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 22:34:29: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 22:34:29: #1 total tags in treatment: 12057787 INFO @ Fri, 10 Dec 2021 22:34:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:34:29: #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 22:34:30: #1 tags after filtering in treatment: 10733826 INFO @ Fri, 10 Dec 2021 22:34:30: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 22:34:30: #1 finished! INFO @ Fri, 10 Dec 2021 22:34:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:34:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:34:31: #2 number of paired peaks: 1226 INFO @ Fri, 10 Dec 2021 22:34:31: start model_add_line... INFO @ Fri, 10 Dec 2021 22:34:31: start X-correlation... INFO @ Fri, 10 Dec 2021 22:34:31: end of X-cor INFO @ Fri, 10 Dec 2021 22:34:31: #2 finished! INFO @ Fri, 10 Dec 2021 22:34:31: #2 predicted fragment length is 159 bps INFO @ Fri, 10 Dec 2021 22:34:31: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 10 Dec 2021 22:34:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.05_model.r WARNING @ Fri, 10 Dec 2021 22:34:31: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:34:31: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Fri, 10 Dec 2021 22:34:31: #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 22:34:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:34:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:34:35: 27000000 INFO @ Fri, 10 Dec 2021 22:34:37: 18000000 INFO @ Fri, 10 Dec 2021 22:34:43: 28000000 INFO @ Fri, 10 Dec 2021 22:34:50: 19000000 INFO @ Fri, 10 Dec 2021 22:34:52: 29000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:34:59: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 22:34:59: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 22:34:59: #1 total tags in treatment: 12057787 INFO @ Fri, 10 Dec 2021 22:34:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:34:59: #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 22:34:59: #1 tags after filtering in treatment: 10733826 INFO @ Fri, 10 Dec 2021 22:34:59: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 22:34:59: #1 finished! INFO @ Fri, 10 Dec 2021 22:34:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:34:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:35:01: #2 number of paired peaks: 1226 INFO @ Fri, 10 Dec 2021 22:35:01: start model_add_line... INFO @ Fri, 10 Dec 2021 22:35:01: start X-correlation... INFO @ Fri, 10 Dec 2021 22:35:01: end of X-cor INFO @ Fri, 10 Dec 2021 22:35:01: #2 finished! INFO @ Fri, 10 Dec 2021 22:35:01: #2 predicted fragment length is 159 bps INFO @ Fri, 10 Dec 2021 22:35:01: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 10 Dec 2021 22:35:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.10_model.r WARNING @ Fri, 10 Dec 2021 22:35:01: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:35:01: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Fri, 10 Dec 2021 22:35:01: #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 22:35:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:35:02: 20000000 INFO @ Fri, 10 Dec 2021 22:35:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:35:14: 21000000 INFO @ Fri, 10 Dec 2021 22:35:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:35:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.05_summits.bed INFO @ Fri, 10 Dec 2021 22:35:22: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11407 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:35:26: 22000000 INFO @ Fri, 10 Dec 2021 22:35:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:35:38: 23000000 INFO @ Fri, 10 Dec 2021 22:35:50: 24000000 INFO @ Fri, 10 Dec 2021 22:35:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:35:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:35:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.10_summits.bed INFO @ Fri, 10 Dec 2021 22:35:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6149 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:36:03: 25000000 INFO @ Fri, 10 Dec 2021 22:36:15: 26000000 INFO @ Fri, 10 Dec 2021 22:36:26: 27000000 INFO @ Fri, 10 Dec 2021 22:36:38: 28000000 INFO @ Fri, 10 Dec 2021 22:36:50: 29000000 INFO @ Fri, 10 Dec 2021 22:37:01: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 22:37:01: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 22:37:01: #1 total tags in treatment: 12057787 INFO @ Fri, 10 Dec 2021 22:37:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:37:01: #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 22:37:01: #1 tags after filtering in treatment: 10733826 INFO @ Fri, 10 Dec 2021 22:37:01: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 22:37:01: #1 finished! INFO @ Fri, 10 Dec 2021 22:37:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:37:02: #2 number of paired peaks: 1226 INFO @ Fri, 10 Dec 2021 22:37:02: start model_add_line... INFO @ Fri, 10 Dec 2021 22:37:03: start X-correlation... INFO @ Fri, 10 Dec 2021 22:37:03: end of X-cor INFO @ Fri, 10 Dec 2021 22:37:03: #2 finished! INFO @ Fri, 10 Dec 2021 22:37:03: #2 predicted fragment length is 159 bps INFO @ Fri, 10 Dec 2021 22:37:03: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 10 Dec 2021 22:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.20_model.r WARNING @ Fri, 10 Dec 2021 22:37:03: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:37:03: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Fri, 10 Dec 2021 22:37:03: #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 22:37:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:37:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:37:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:37:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:37:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978863/ERX3978863.20_summits.bed INFO @ Fri, 10 Dec 2021 22:37:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2364 records, 4 fields): 7 millis CompletedMACS2peakCalling