Job ID = 12266650 SRX = SRX7806722 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8670043 spots for SRR11186388/SRR11186388.sra Written 8670043 spots for SRR11186388/SRR11186388.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266930 ("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: 00:17:56 8670043 reads; of these: 8670043 (100.00%) were paired; of these: 4568748 (52.70%) aligned concordantly 0 times 2826435 (32.60%) aligned concordantly exactly 1 time 1274860 (14.70%) aligned concordantly >1 times ---- 4568748 pairs aligned concordantly 0 times; of these: 635575 (13.91%) aligned discordantly 1 time ---- 3933173 pairs aligned 0 times concordantly or discordantly; of these: 7866346 mates make up the pairs; of these: 7059183 (89.74%) aligned 0 times 330956 (4.21%) aligned exactly 1 time 476207 (6.05%) aligned >1 times 59.29% overall alignment rate Time searching: 00:17:56 Overall time: 00:17:56 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 8 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] 503391 / 4705540 = 0.1070 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.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, 03 Apr 2021 09:26:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:26:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:26:53: 1000000 INFO @ Sat, 03 Apr 2021 09:27:00: 2000000 INFO @ Sat, 03 Apr 2021 09:27:07: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:27:14: 4000000 INFO @ Sat, 03 Apr 2021 09:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.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, 03 Apr 2021 09:27:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:27:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:27:22: 5000000 INFO @ Sat, 03 Apr 2021 09:27:24: 1000000 INFO @ Sat, 03 Apr 2021 09:27:29: 6000000 INFO @ Sat, 03 Apr 2021 09:27:32: 2000000 INFO @ Sat, 03 Apr 2021 09:27:37: 7000000 INFO @ Sat, 03 Apr 2021 09:27:40: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:27:45: 8000000 INFO @ Sat, 03 Apr 2021 09:27:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.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, 03 Apr 2021 09:27:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:27:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:27:48: 4000000 INFO @ Sat, 03 Apr 2021 09:27:53: 9000000 INFO @ Sat, 03 Apr 2021 09:27:54: 1000000 INFO @ Sat, 03 Apr 2021 09:27:55: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:27:55: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:27:55: #1 total tags in treatment: 3629122 INFO @ Sat, 03 Apr 2021 09:27:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:27:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:27:55: #1 tags after filtering in treatment: 3190636 INFO @ Sat, 03 Apr 2021 09:27:55: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 09:27:55: #1 finished! INFO @ Sat, 03 Apr 2021 09:27:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:27:55: #2 number of paired peaks: 1028 INFO @ Sat, 03 Apr 2021 09:27:55: start model_add_line... INFO @ Sat, 03 Apr 2021 09:27:55: start X-correlation... INFO @ Sat, 03 Apr 2021 09:27:55: end of X-cor INFO @ Sat, 03 Apr 2021 09:27:55: #2 finished! INFO @ Sat, 03 Apr 2021 09:27:55: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 09:27:55: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Apr 2021 09:27:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.05_model.r WARNING @ Sat, 03 Apr 2021 09:27:55: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:27:55: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 03 Apr 2021 09:27:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:27:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:27:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:27:56: 5000000 INFO @ Sat, 03 Apr 2021 09:28:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:28:03: 2000000 INFO @ Sat, 03 Apr 2021 09:28:04: 6000000 INFO @ Sat, 03 Apr 2021 09:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.05_summits.bed INFO @ Sat, 03 Apr 2021 09:28:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3282 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:28:10: 3000000 INFO @ Sat, 03 Apr 2021 09:28:11: 7000000 INFO @ Sat, 03 Apr 2021 09:28:18: 4000000 INFO @ Sat, 03 Apr 2021 09:28:19: 8000000 INFO @ Sat, 03 Apr 2021 09:28:26: 5000000 INFO @ Sat, 03 Apr 2021 09:28:27: 9000000 INFO @ Sat, 03 Apr 2021 09:28:29: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:28:29: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:28:29: #1 total tags in treatment: 3629122 INFO @ Sat, 03 Apr 2021 09:28:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:28:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:28:29: #1 tags after filtering in treatment: 3190636 INFO @ Sat, 03 Apr 2021 09:28:29: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 09:28:29: #1 finished! INFO @ Sat, 03 Apr 2021 09:28:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:28:29: #2 number of paired peaks: 1028 INFO @ Sat, 03 Apr 2021 09:28:29: start model_add_line... INFO @ Sat, 03 Apr 2021 09:28:29: start X-correlation... INFO @ Sat, 03 Apr 2021 09:28:29: end of X-cor INFO @ Sat, 03 Apr 2021 09:28:29: #2 finished! INFO @ Sat, 03 Apr 2021 09:28:29: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 09:28:29: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Apr 2021 09:28:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.10_model.r WARNING @ Sat, 03 Apr 2021 09:28:29: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:28:29: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 03 Apr 2021 09:28:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:28:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:28:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:28:33: 6000000 INFO @ Sat, 03 Apr 2021 09:28:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.10_summits.bed INFO @ Sat, 03 Apr 2021 09:28:40: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (974 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:28:40: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:28:47: 8000000 INFO @ Sat, 03 Apr 2021 09:28:54: 9000000 INFO @ Sat, 03 Apr 2021 09:28:56: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:28:56: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:28:56: #1 total tags in treatment: 3629122 INFO @ Sat, 03 Apr 2021 09:28:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:28:56: #1 tags after filtering in treatment: 3190636 INFO @ Sat, 03 Apr 2021 09:28:56: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 03 Apr 2021 09:28:56: #1 finished! INFO @ Sat, 03 Apr 2021 09:28:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:28:57: #2 number of paired peaks: 1028 INFO @ Sat, 03 Apr 2021 09:28:57: start model_add_line... INFO @ Sat, 03 Apr 2021 09:28:57: start X-correlation... INFO @ Sat, 03 Apr 2021 09:28:57: end of X-cor INFO @ Sat, 03 Apr 2021 09:28:57: #2 finished! INFO @ Sat, 03 Apr 2021 09:28:57: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Apr 2021 09:28:57: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Apr 2021 09:28:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.20_model.r WARNING @ Sat, 03 Apr 2021 09:28:57: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:28:57: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 03 Apr 2021 09:28:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:28:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:29:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:29:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:29:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:29:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806722/SRX7806722.20_summits.bed INFO @ Sat, 03 Apr 2021 09:29:07: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (215 records, 4 fields): 3 millis CompletedMACS2peakCalling