Job ID = 14159456 SRX = SRX8845620 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6930381 spots for SRR12345965/SRR12345965.sra Written 6930381 spots for SRR12345965/SRR12345965.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159658 ("srTce11") 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: 00:06:13 6930381 reads; of these: 6930381 (100.00%) were paired; of these: 2345780 (33.85%) aligned concordantly 0 times 3839244 (55.40%) aligned concordantly exactly 1 time 745357 (10.75%) aligned concordantly >1 times ---- 2345780 pairs aligned concordantly 0 times; of these: 688560 (29.35%) aligned discordantly 1 time ---- 1657220 pairs aligned 0 times concordantly or discordantly; of these: 3314440 mates make up the pairs; of these: 2852867 (86.07%) aligned 0 times 196707 (5.93%) aligned exactly 1 time 264866 (7.99%) aligned >1 times 79.42% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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 8 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] 748056 / 5226518 = 0.1431 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 @ Wed, 08 Dec 2021 22:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.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 @ Wed, 08 Dec 2021 22:15:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:15:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:15:13: 1000000 INFO @ Wed, 08 Dec 2021 22:15:18: 2000000 INFO @ Wed, 08 Dec 2021 22:15:23: 3000000 INFO @ Wed, 08 Dec 2021 22:15:28: 4000000 INFO @ Wed, 08 Dec 2021 22:15:33: 5000000 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 @ Wed, 08 Dec 2021 22:15:38: 6000000 INFO @ Wed, 08 Dec 2021 22:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.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 @ Wed, 08 Dec 2021 22:15:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:15:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:15:43: 7000000 INFO @ Wed, 08 Dec 2021 22:15:43: 1000000 INFO @ Wed, 08 Dec 2021 22:15:49: 8000000 INFO @ Wed, 08 Dec 2021 22:15:49: 2000000 INFO @ Wed, 08 Dec 2021 22:15:54: 9000000 INFO @ Wed, 08 Dec 2021 22:15:54: 3000000 INFO @ Wed, 08 Dec 2021 22:15:57: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:15:57: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:15:57: #1 total tags in treatment: 3925709 INFO @ Wed, 08 Dec 2021 22:15:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:15:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:15:57: #1 tags after filtering in treatment: 2892428 INFO @ Wed, 08 Dec 2021 22:15:57: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 22:15:57: #1 finished! INFO @ Wed, 08 Dec 2021 22:15:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:15:57: #2 number of paired peaks: 3319 INFO @ Wed, 08 Dec 2021 22:15:57: start model_add_line... INFO @ Wed, 08 Dec 2021 22:15:57: start X-correlation... INFO @ Wed, 08 Dec 2021 22:15:57: end of X-cor INFO @ Wed, 08 Dec 2021 22:15:57: #2 finished! INFO @ Wed, 08 Dec 2021 22:15:57: #2 predicted fragment length is 117 bps INFO @ Wed, 08 Dec 2021 22:15:57: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 08 Dec 2021 22:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.05_model.r WARNING @ Wed, 08 Dec 2021 22:15:57: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:15:57: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 08 Dec 2021 22:15:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:15:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:16:00: 4000000 INFO @ Wed, 08 Dec 2021 22:16:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:16:05: 5000000 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 @ Wed, 08 Dec 2021 22:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.05_summits.bed INFO @ Wed, 08 Dec 2021 22:16:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6478 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.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 @ Wed, 08 Dec 2021 22:16:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:16:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:16:10: 6000000 INFO @ Wed, 08 Dec 2021 22:16:13: 1000000 INFO @ Wed, 08 Dec 2021 22:16:16: 7000000 INFO @ Wed, 08 Dec 2021 22:16:19: 2000000 INFO @ Wed, 08 Dec 2021 22:16:21: 8000000 INFO @ Wed, 08 Dec 2021 22:16:24: 3000000 INFO @ Wed, 08 Dec 2021 22:16:27: 9000000 INFO @ Wed, 08 Dec 2021 22:16:29: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:16:29: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:16:29: #1 total tags in treatment: 3925709 INFO @ Wed, 08 Dec 2021 22:16:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:16:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:16:29: #1 tags after filtering in treatment: 2892428 INFO @ Wed, 08 Dec 2021 22:16:29: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 22:16:29: #1 finished! INFO @ Wed, 08 Dec 2021 22:16:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:16:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:16:30: 4000000 INFO @ Wed, 08 Dec 2021 22:16:30: #2 number of paired peaks: 3319 INFO @ Wed, 08 Dec 2021 22:16:30: start model_add_line... INFO @ Wed, 08 Dec 2021 22:16:30: start X-correlation... INFO @ Wed, 08 Dec 2021 22:16:30: end of X-cor INFO @ Wed, 08 Dec 2021 22:16:30: #2 finished! INFO @ Wed, 08 Dec 2021 22:16:30: #2 predicted fragment length is 117 bps INFO @ Wed, 08 Dec 2021 22:16:30: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 08 Dec 2021 22:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.10_model.r WARNING @ Wed, 08 Dec 2021 22:16:30: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:16:30: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 08 Dec 2021 22:16:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:16:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:16:35: 5000000 INFO @ Wed, 08 Dec 2021 22:16:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.10_summits.bed INFO @ Wed, 08 Dec 2021 22:16:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4128 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:16:40: 6000000 INFO @ Wed, 08 Dec 2021 22:16:45: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:16:51: 8000000 INFO @ Wed, 08 Dec 2021 22:16:56: 9000000 INFO @ Wed, 08 Dec 2021 22:16:59: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:16:59: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:16:59: #1 total tags in treatment: 3925709 INFO @ Wed, 08 Dec 2021 22:16:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:16:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:16:59: #1 tags after filtering in treatment: 2892428 INFO @ Wed, 08 Dec 2021 22:16:59: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 22:16:59: #1 finished! INFO @ Wed, 08 Dec 2021 22:16:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:16:59: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:16:59: #2 number of paired peaks: 3319 INFO @ Wed, 08 Dec 2021 22:16:59: start model_add_line... INFO @ Wed, 08 Dec 2021 22:16:59: start X-correlation... INFO @ Wed, 08 Dec 2021 22:16:59: end of X-cor INFO @ Wed, 08 Dec 2021 22:16:59: #2 finished! INFO @ Wed, 08 Dec 2021 22:16:59: #2 predicted fragment length is 117 bps INFO @ Wed, 08 Dec 2021 22:16:59: #2 alternative fragment length(s) may be 117 bps INFO @ Wed, 08 Dec 2021 22:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.20_model.r WARNING @ Wed, 08 Dec 2021 22:16:59: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:16:59: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Wed, 08 Dec 2021 22:16:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:16:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:17:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845620/SRX8845620.20_summits.bed INFO @ Wed, 08 Dec 2021 22:17:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2228 records, 4 fields): 4 millis CompletedMACS2peakCalling