Job ID = 12264773 SRX = SRX4029336 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24327078 spots for SRR7100996/SRR7100996.sra Written 24327078 spots for SRR7100996/SRR7100996.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265398 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:31:20 24327078 reads; of these: 24327078 (100.00%) were paired; of these: 11783460 (48.44%) aligned concordantly 0 times 10064982 (41.37%) aligned concordantly exactly 1 time 2478636 (10.19%) aligned concordantly >1 times ---- 11783460 pairs aligned concordantly 0 times; of these: 1913255 (16.24%) aligned discordantly 1 time ---- 9870205 pairs aligned 0 times concordantly or discordantly; of these: 19740410 mates make up the pairs; of these: 17789849 (90.12%) aligned 0 times 855380 (4.33%) aligned exactly 1 time 1095181 (5.55%) aligned >1 times 63.44% overall alignment rate Time searching: 00:31:21 Overall time: 00:31:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 7932613 / 14364336 = 0.5522 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 06:35:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:35:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:35:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:35:35: 1000000 INFO @ Sat, 03 Apr 2021 06:35:41: 2000000 INFO @ Sat, 03 Apr 2021 06:35:46: 3000000 INFO @ Sat, 03 Apr 2021 06:35:51: 4000000 INFO @ Sat, 03 Apr 2021 06:35:56: 5000000 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 06:35:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:35:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:35:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:36:02: 6000000 INFO @ Sat, 03 Apr 2021 06:36:05: 1000000 INFO @ Sat, 03 Apr 2021 06:36:08: 7000000 INFO @ Sat, 03 Apr 2021 06:36:11: 2000000 INFO @ Sat, 03 Apr 2021 06:36:14: 8000000 INFO @ Sat, 03 Apr 2021 06:36:17: 3000000 INFO @ Sat, 03 Apr 2021 06:36:20: 9000000 INFO @ Sat, 03 Apr 2021 06:36:23: 4000000 INFO @ Sat, 03 Apr 2021 06:36:26: 10000000 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 06:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:36:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:36:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:36:29: 5000000 INFO @ Sat, 03 Apr 2021 06:36:32: 11000000 INFO @ Sat, 03 Apr 2021 06:36:35: 1000000 INFO @ Sat, 03 Apr 2021 06:36:35: 6000000 INFO @ Sat, 03 Apr 2021 06:36:37: 12000000 INFO @ Sat, 03 Apr 2021 06:36:41: 2000000 INFO @ Sat, 03 Apr 2021 06:36:41: 7000000 INFO @ Sat, 03 Apr 2021 06:36:43: 13000000 INFO @ Sat, 03 Apr 2021 06:36:46: 3000000 INFO @ Sat, 03 Apr 2021 06:36:47: 8000000 INFO @ Sat, 03 Apr 2021 06:36:49: 14000000 INFO @ Sat, 03 Apr 2021 06:36:52: 4000000 INFO @ Sat, 03 Apr 2021 06:36:53: 9000000 INFO @ Sat, 03 Apr 2021 06:36:55: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:36:55: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:36:55: #1 total tags in treatment: 5398131 INFO @ Sat, 03 Apr 2021 06:36:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:36:55: #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 06:36:55: #1 tags after filtering in treatment: 3328735 INFO @ Sat, 03 Apr 2021 06:36:55: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 06:36:55: #1 finished! INFO @ Sat, 03 Apr 2021 06:36:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:36:55: #2 number of paired peaks: 3151 INFO @ Sat, 03 Apr 2021 06:36:55: start model_add_line... INFO @ Sat, 03 Apr 2021 06:36:55: start X-correlation... INFO @ Sat, 03 Apr 2021 06:36:55: end of X-cor INFO @ Sat, 03 Apr 2021 06:36:55: #2 finished! INFO @ Sat, 03 Apr 2021 06:36:55: #2 predicted fragment length is 118 bps INFO @ Sat, 03 Apr 2021 06:36:55: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 03 Apr 2021 06:36:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.05_model.r WARNING @ Sat, 03 Apr 2021 06:36:55: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:36:55: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 03 Apr 2021 06:36:55: #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 06:36:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:36:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:36:57: 5000000 INFO @ Sat, 03 Apr 2021 06:36:59: 10000000 INFO @ Sat, 03 Apr 2021 06:37:03: 6000000 INFO @ Sat, 03 Apr 2021 06:37:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:37:05: 11000000 INFO @ Sat, 03 Apr 2021 06:37:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:37:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:37:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.05_summits.bed INFO @ Sat, 03 Apr 2021 06:37:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5238 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:37:09: 7000000 INFO @ Sat, 03 Apr 2021 06:37:10: 12000000 INFO @ Sat, 03 Apr 2021 06:37:15: 8000000 INFO @ Sat, 03 Apr 2021 06:37:16: 13000000 INFO @ Sat, 03 Apr 2021 06:37:20: 9000000 INFO @ Sat, 03 Apr 2021 06:37:21: 14000000 INFO @ Sat, 03 Apr 2021 06:37:26: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:37:26: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:37:26: #1 total tags in treatment: 5398131 INFO @ Sat, 03 Apr 2021 06:37:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:37:26: #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 06:37:26: #1 tags after filtering in treatment: 3328735 INFO @ Sat, 03 Apr 2021 06:37:26: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 06:37:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:37:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:37:26: 10000000 INFO @ Sat, 03 Apr 2021 06:37:26: #2 number of paired peaks: 3151 INFO @ Sat, 03 Apr 2021 06:37:26: start model_add_line... INFO @ Sat, 03 Apr 2021 06:37:26: start X-correlation... INFO @ Sat, 03 Apr 2021 06:37:26: end of X-cor INFO @ Sat, 03 Apr 2021 06:37:26: #2 finished! INFO @ Sat, 03 Apr 2021 06:37:26: #2 predicted fragment length is 118 bps INFO @ Sat, 03 Apr 2021 06:37:26: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 03 Apr 2021 06:37:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.10_model.r WARNING @ Sat, 03 Apr 2021 06:37:26: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:37:26: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 03 Apr 2021 06:37:26: #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 06:37:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:37:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:37:31: 11000000 INFO @ Sat, 03 Apr 2021 06:37:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:37:37: 12000000 INFO @ Sat, 03 Apr 2021 06:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.10_summits.bed INFO @ Sat, 03 Apr 2021 06:37:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3113 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:37:42: 13000000 INFO @ Sat, 03 Apr 2021 06:37:48: 14000000 INFO @ Sat, 03 Apr 2021 06:37:53: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:37:53: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:37:53: #1 total tags in treatment: 5398131 INFO @ Sat, 03 Apr 2021 06:37:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:37:53: #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 06:37:53: #1 tags after filtering in treatment: 3328735 INFO @ Sat, 03 Apr 2021 06:37:53: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 03 Apr 2021 06:37:53: #1 finished! INFO @ Sat, 03 Apr 2021 06:37:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:37:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:37:53: #2 number of paired peaks: 3151 INFO @ Sat, 03 Apr 2021 06:37:53: start model_add_line... INFO @ Sat, 03 Apr 2021 06:37:53: start X-correlation... INFO @ Sat, 03 Apr 2021 06:37:53: end of X-cor INFO @ Sat, 03 Apr 2021 06:37:53: #2 finished! INFO @ Sat, 03 Apr 2021 06:37:53: #2 predicted fragment length is 118 bps INFO @ Sat, 03 Apr 2021 06:37:53: #2 alternative fragment length(s) may be 118 bps INFO @ Sat, 03 Apr 2021 06:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.20_model.r WARNING @ Sat, 03 Apr 2021 06:37:54: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:37:54: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Sat, 03 Apr 2021 06:37:54: #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 06:37:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:37:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:38:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:38:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:38:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:38:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4029336/SRX4029336.20_summits.bed INFO @ Sat, 03 Apr 2021 06:38:05: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (1411 records, 4 fields): 3 millis CompletedMACS2peakCalling