[2024-01-24 13:58:10,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg630f9933-c2aa-4e23-a792-7d53919d7c72/dqc_reference
[2024-01-24 13:58:12,115] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,116] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,116] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f9d727e-7722-4242-a6ff-bff9c2f52bbc/GCF_003347595.2_ASM334759v2_genomic.fna.gz | prodigal -d GCF_003347595.2_ASM334759v2_genomic.fna/cds.fna -a GCF_003347595.2_ASM334759v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:41,877] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:41,878] [INFO] Task started: HMMsearch
[2024-01-24 13:58:41,878] [INFO] Running command: hmmsearch --tblout GCF_003347595.2_ASM334759v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg630f9933-c2aa-4e23-a792-7d53919d7c72/dqc_reference/reference_markers.hmm GCF_003347595.2_ASM334759v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:42,184] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:42,186] [INFO] Found 6/6 markers.
[2024-01-24 13:58:42,235] [INFO] Query marker FASTA was written to GCF_003347595.2_ASM334759v2_genomic.fna/markers.fasta
[2024-01-24 13:58:42,235] [INFO] Task started: Blastn
[2024-01-24 13:58:42,235] [INFO] Running command: blastn -query GCF_003347595.2_ASM334759v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg630f9933-c2aa-4e23-a792-7d53919d7c72/dqc_reference/reference_markers.fasta -out GCF_003347595.2_ASM334759v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:42,908] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:42,912] [INFO] Selected 19 target genomes.
[2024-01-24 13:58:42,912] [INFO] Target genome list was writen to GCF_003347595.2_ASM334759v2_genomic.fna/target_genomes.txt
[2024-01-24 13:58:42,924] [INFO] Task started: fastANI
[2024-01-24 13:58:42,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9d727e-7722-4242-a6ff-bff9c2f52bbc/GCF_003347595.2_ASM334759v2_genomic.fna.gz --refList GCF_003347595.2_ASM334759v2_genomic.fna/target_genomes.txt --output GCF_003347595.2_ASM334759v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:00,450] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:00,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg630f9933-c2aa-4e23-a792-7d53919d7c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:00,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg630f9933-c2aa-4e23-a792-7d53919d7c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:00,467] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:00,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:00,468] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Botryobacter ruber	strain=SYSU D60016	GCA_003347595.2	2171629	2171629	type	True	100.0	1911	1919	95	conclusive
Pontibacter beigongshangensis	strain=T6-1	GCA_014332515.1	2574733	2574733	type	True	78.4364	668	1919	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.1887	471	1919	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	77.994	411	1919	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	77.9815	452	1919	95	below_threshold
Pontibacter indicus	strain=LP100	GCA_900156345.1	1317125	1317125	type	True	77.9635	404	1919	95	below_threshold
Pontibacter russatus	strain=BT326	GCA_009931655.1	2694929	2694929	type	True	77.9015	464	1919	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	77.8553	462	1919	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	77.7918	400	1919	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	77.767	424	1919	95	below_threshold
Pontibacter roseus	strain=DSM 17521	GCA_000373265.1	336989	336989	type	True	77.7574	414	1919	95	below_threshold
Pontibacter akesuensis	strain=AKS 1T	GCA_001611675.1	388950	388950	type	True	77.7191	400	1919	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	77.707	452	1919	95	below_threshold
Pontibacter akesuensis	strain=DSM 18820	GCA_900116885.1	388950	388950	type	True	77.6477	402	1919	95	below_threshold
Pontibacter lucknowensis	strain=DM9	GCA_900156415.1	1077936	1077936	type	True	77.6299	373	1919	95	below_threshold
Pontibacter amylolyticus	strain=CGMCC 1.12749	GCA_014638845.1	1424080	1424080	type	True	77.6188	431	1919	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.4577	261	1919	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.3575	281	1919	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.2916	212	1919	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:00,469] [INFO] DFAST Taxonomy check result was written to GCF_003347595.2_ASM334759v2_genomic.fna/tc_result.tsv
[2024-01-24 13:59:00,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:00,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:00,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg630f9933-c2aa-4e23-a792-7d53919d7c72/dqc_reference/checkm_data
[2024-01-24 13:59:00,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:00,526] [INFO] Task started: CheckM
[2024-01-24 13:59:00,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003347595.2_ASM334759v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003347595.2_ASM334759v2_genomic.fna/checkm_input GCF_003347595.2_ASM334759v2_genomic.fna/checkm_result
[2024-01-24 14:00:17,502] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:17,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:17,529] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:17,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:17,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003347595.2_ASM334759v2_genomic.fna/markers.fasta)
[2024-01-24 14:00:17,530] [INFO] Task started: Blastn
[2024-01-24 14:00:17,530] [INFO] Running command: blastn -query GCF_003347595.2_ASM334759v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg630f9933-c2aa-4e23-a792-7d53919d7c72/dqc_reference/reference_markers_gtdb.fasta -out GCF_003347595.2_ASM334759v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:18,425] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:18,429] [INFO] Selected 15 target genomes.
[2024-01-24 14:00:18,429] [INFO] Target genome list was writen to GCF_003347595.2_ASM334759v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:18,451] [INFO] Task started: fastANI
[2024-01-24 14:00:18,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f9d727e-7722-4242-a6ff-bff9c2f52bbc/GCF_003347595.2_ASM334759v2_genomic.fna.gz --refList GCF_003347595.2_ASM334759v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003347595.2_ASM334759v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:33,637] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:33,654] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:33,655] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003347595.2	s__Botryobacter ruber	100.0	1911	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014332515.1	s__Botryobacter beigongshangensis	78.4363	668	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017455.1	s__Botryobacter sp008017455	78.3932	586	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003585765.1	s__Pontibacter actiniarum	78.0447	408	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900156345.1	s__Pontibacter indicus	77.9706	402	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385705.1	s__Pontibacter sp006385705	77.9641	455	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907195.1	s__Pontibacter sp001907195	77.8623	461	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846395.1	s__Pontibacter ramchanderi	77.7998	399	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113285.1	s__Pontibacter chinhatensis	77.7824	422	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373265.1	s__Pontibacter roseus	77.7655	413	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611675.1	s__Pontibacter akesuensis	77.7111	401	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003054055.1	s__Pontibacter mucosus	77.6929	454	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694705.1	s__Pontibacter sp015694705	77.6742	387	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491705.1	s__SGAir0037 sp005491705	77.6166	283	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__SGAir0037	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638845.1	s__Pontibacter amylolyticus	77.614	433	1919	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:33,659] [INFO] GTDB search result was written to GCF_003347595.2_ASM334759v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:33,660] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:33,664] [INFO] DFAST_QC result json was written to GCF_003347595.2_ASM334759v2_genomic.fna/dqc_result.json
[2024-01-24 14:00:33,664] [INFO] DFAST_QC completed!
[2024-01-24 14:00:33,664] [INFO] Total running time: 0h2m23s