[2024-01-24 14:05:36,627] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,633] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,634] [INFO] DQC Reference Directory: /var/lib/cwl/stge9a7504d-1106-4a24-92ca-aa1af35f0de4/dqc_reference
[2024-01-24 14:05:37,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,947] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg7324f1a0-9bee-4e19-be2d-73db631ba1f9/GCF_016307205.1_ASM1630720v1_genomic.fna.gz | prodigal -d GCF_016307205.1_ASM1630720v1_genomic.fna/cds.fna -a GCF_016307205.1_ASM1630720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:47,905] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:47,906] [INFO] Task started: HMMsearch
[2024-01-24 14:05:47,906] [INFO] Running command: hmmsearch --tblout GCF_016307205.1_ASM1630720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9a7504d-1106-4a24-92ca-aa1af35f0de4/dqc_reference/reference_markers.hmm GCF_016307205.1_ASM1630720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:48,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:48,204] [INFO] Found 6/6 markers.
[2024-01-24 14:05:48,232] [INFO] Query marker FASTA was written to GCF_016307205.1_ASM1630720v1_genomic.fna/markers.fasta
[2024-01-24 14:05:48,232] [INFO] Task started: Blastn
[2024-01-24 14:05:48,232] [INFO] Running command: blastn -query GCF_016307205.1_ASM1630720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9a7504d-1106-4a24-92ca-aa1af35f0de4/dqc_reference/reference_markers.fasta -out GCF_016307205.1_ASM1630720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:49,104] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:49,107] [INFO] Selected 25 target genomes.
[2024-01-24 14:05:49,107] [INFO] Target genome list was writen to GCF_016307205.1_ASM1630720v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:49,117] [INFO] Task started: fastANI
[2024-01-24 14:05:49,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg7324f1a0-9bee-4e19-be2d-73db631ba1f9/GCF_016307205.1_ASM1630720v1_genomic.fna.gz --refList GCF_016307205.1_ASM1630720v1_genomic.fna/target_genomes.txt --output GCF_016307205.1_ASM1630720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:07,273] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9a7504d-1106-4a24-92ca-aa1af35f0de4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:07,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9a7504d-1106-4a24-92ca-aa1af35f0de4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:07,291] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:07,292] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:07,292] [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
Pontibaca salina	strain=S1109L	GCA_016307205.1	2795731	2795731	type	True	100.0	960	962	95	conclusive
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	77.9299	330	962	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.7876	323	962	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.711	298	962	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.6286	327	962	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	77.4905	320	962	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	77.4166	255	962	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.3985	277	962	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.3801	275	962	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.2478	228	962	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	77.2378	221	962	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.2177	254	962	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.2113	253	962	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	77.1725	245	962	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.1094	264	962	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0725	149	962	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.0719	202	962	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.9795	203	962	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.9269	201	962	95	below_threshold
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	76.8674	192	962	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	76.8271	195	962	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8172	201	962	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.742	147	962	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.6806	154	962	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	76.6249	220	962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,294] [INFO] DFAST Taxonomy check result was written to GCF_016307205.1_ASM1630720v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:07,294] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:07,294] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:07,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9a7504d-1106-4a24-92ca-aa1af35f0de4/dqc_reference/checkm_data
[2024-01-24 14:06:07,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:07,327] [INFO] Task started: CheckM
[2024-01-24 14:06:07,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016307205.1_ASM1630720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016307205.1_ASM1630720v1_genomic.fna/checkm_input GCF_016307205.1_ASM1630720v1_genomic.fna/checkm_result
[2024-01-24 14:06:40,315] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:40,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:40,336] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:40,337] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:40,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016307205.1_ASM1630720v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:40,338] [INFO] Task started: Blastn
[2024-01-24 14:06:40,338] [INFO] Running command: blastn -query GCF_016307205.1_ASM1630720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9a7504d-1106-4a24-92ca-aa1af35f0de4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016307205.1_ASM1630720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:41,696] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:41,705] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:41,706] [INFO] Target genome list was writen to GCF_016307205.1_ASM1630720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:41,738] [INFO] Task started: fastANI
[2024-01-24 14:06:41,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg7324f1a0-9bee-4e19-be2d-73db631ba1f9/GCF_016307205.1_ASM1630720v1_genomic.fna.gz --refList GCF_016307205.1_ASM1630720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016307205.1_ASM1630720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:59,875] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:59,899] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:59,900] [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_016307205.1	s__Pontibaca sp016307205	100.0	960	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontibaca	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002786325.1	s__Pseudooceanicola_C lipolyticus	78.0304	302	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156525.1	s__Pontibaca methylaminivorans	77.9319	331	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontibaca	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.9082	317	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016521575.1	s__Sedimentitalea sp016521575	77.8611	288	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.8038	322	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	77.7914	296	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005938225.1	s__Arenibacterium halophilum	77.7361	278	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	77.6025	328	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_900142185.1	s__Lutimaribacter pacificus	77.5632	292	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004348975.1	s__Antarcticimicrobium sediminis	77.4905	320	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	77.4157	206	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	77.3908	274	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	77.3562	255	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.2564	261	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313245.1	s__Primorskyibacter marinus	77.2373	221	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500245.1	s__Ruegeria_B sp010500245	77.2332	293	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.2161	255	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.1317	212	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.118	268	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	76.9715	216	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.8992	195	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_007923445.1	s__Puniceibacterium confluentis	76.8271	196	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	76.8001	174	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:59,901] [INFO] GTDB search result was written to GCF_016307205.1_ASM1630720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:59,902] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:59,906] [INFO] DFAST_QC result json was written to GCF_016307205.1_ASM1630720v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:59,906] [INFO] DFAST_QC completed!
[2024-01-24 14:06:59,906] [INFO] Total running time: 0h1m23s