[2024-01-25 17:34:07,128] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,138] [INFO] DQC Reference Directory: /var/lib/cwl/stg939d709f-7780-471b-8046-3a4d9877a094/dqc_reference
[2024-01-25 17:34:09,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,029] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg84af851f-5ec5-4f0f-81c2-6b54439755a8/GCF_003385715.1_ASM338571v1_genomic.fna.gz | prodigal -d GCF_003385715.1_ASM338571v1_genomic.fna/cds.fna -a GCF_003385715.1_ASM338571v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:19,058] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:19,058] [INFO] Task started: HMMsearch
[2024-01-25 17:34:19,058] [INFO] Running command: hmmsearch --tblout GCF_003385715.1_ASM338571v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg939d709f-7780-471b-8046-3a4d9877a094/dqc_reference/reference_markers.hmm GCF_003385715.1_ASM338571v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:19,294] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:19,295] [INFO] Found 6/6 markers.
[2024-01-25 17:34:19,322] [INFO] Query marker FASTA was written to GCF_003385715.1_ASM338571v1_genomic.fna/markers.fasta
[2024-01-25 17:34:19,322] [INFO] Task started: Blastn
[2024-01-25 17:34:19,323] [INFO] Running command: blastn -query GCF_003385715.1_ASM338571v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg939d709f-7780-471b-8046-3a4d9877a094/dqc_reference/reference_markers.fasta -out GCF_003385715.1_ASM338571v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:20,140] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:20,143] [INFO] Selected 20 target genomes.
[2024-01-25 17:34:20,143] [INFO] Target genome list was writen to GCF_003385715.1_ASM338571v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:20,467] [INFO] Task started: fastANI
[2024-01-25 17:34:20,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg84af851f-5ec5-4f0f-81c2-6b54439755a8/GCF_003385715.1_ASM338571v1_genomic.fna.gz --refList GCF_003385715.1_ASM338571v1_genomic.fna/target_genomes.txt --output GCF_003385715.1_ASM338571v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:34,118] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:34,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg939d709f-7780-471b-8046-3a4d9877a094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:34,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg939d709f-7780-471b-8046-3a4d9877a094/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:34,129] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:34,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:34,130] [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
Pontivivens insulae	strain=DSM 103361	GCA_003385715.1	1639689	1639689	type	True	100.0	1175	1176	95	conclusive
Pontivivens insulae	strain=CeCT 8812	GCA_900302495.1	1639689	1639689	type	True	99.9998	1176	1176	95	conclusive
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	78.1914	348	1176	95	below_threshold
Rubricella aquisinus	strain=DSM 103377	GCA_014199445.1	2028108	2028108	type	True	77.2094	224	1176	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	77.113	131	1176	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.074	133	1176	95	below_threshold
Oceanomicrobium pacificus	strain=KN286	GCA_009833495.1	2692916	2692916	type	True	77.0654	174	1176	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.0435	124	1176	95	below_threshold
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	77.0117	141	1176	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9701	147	1176	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	76.9156	137	1176	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	76.8949	130	1176	95	below_threshold
Boseongicola aestuarii	strain=CECT 8489	GCA_900184815.1	1470561	1470561	type	True	76.7865	85	1176	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.7715	171	1176	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	76.678	137	1176	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	76.6457	170	1176	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	76.6386	113	1176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:34,131] [INFO] DFAST Taxonomy check result was written to GCF_003385715.1_ASM338571v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:34,132] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:34,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:34,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg939d709f-7780-471b-8046-3a4d9877a094/dqc_reference/checkm_data
[2024-01-25 17:34:34,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:34,168] [INFO] Task started: CheckM
[2024-01-25 17:34:34,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385715.1_ASM338571v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385715.1_ASM338571v1_genomic.fna/checkm_input GCF_003385715.1_ASM338571v1_genomic.fna/checkm_result
[2024-01-25 17:35:06,263] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:06,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:06,282] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:06,282] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:06,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385715.1_ASM338571v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:06,283] [INFO] Task started: Blastn
[2024-01-25 17:35:06,283] [INFO] Running command: blastn -query GCF_003385715.1_ASM338571v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg939d709f-7780-471b-8046-3a4d9877a094/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385715.1_ASM338571v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:07,936] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:07,946] [INFO] Selected 21 target genomes.
[2024-01-25 17:35:07,946] [INFO] Target genome list was writen to GCF_003385715.1_ASM338571v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:07,957] [INFO] Task started: fastANI
[2024-01-25 17:35:07,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg84af851f-5ec5-4f0f-81c2-6b54439755a8/GCF_003385715.1_ASM338571v1_genomic.fna.gz --refList GCF_003385715.1_ASM338571v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385715.1_ASM338571v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:22,338] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:22,354] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:22,354] [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_900302495.1	s__Pontivivens insulae	99.9998	1176	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pontivivens	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_015679265.1	s__MT2928 sp015679265	78.1914	348	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MT2928	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290545.1	s__Monaibacterium sp011290545	78.0411	306	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	96.75	96.75	0.88	0.88	2	-
GCF_900231835.1	s__Monaibacterium marinum	77.7637	264	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Monaibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199445.1	s__Rubricella aquisinus	77.2211	223	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubricella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	77.074	133	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009363795.1	s__Palleronia sp900609015	77.0731	116	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003129565.1	s__Salibaculum griseiflavum	77.0117	141	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114635.1	s__Shimia aestuarii	76.972	135	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	76.9535	150	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	76.9156	137	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285435.1	s__Actibacterium ureilyticum	76.8724	174	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	76.8548	152	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	76.7499	165	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359765.1	s__Roseovarius sp014359765	76.6954	120	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113695.1	s__Albimonas pacifica	76.678	137	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	76.6457	170	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_007004065.1	s__Palleronia caenipelagi	76.6386	113	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048875.1	s__Rhodovulum sp011048875	76.5938	99	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359745.1	s__JACIYW01 sp014359745	76.185	101	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JACIYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	76.0236	90	1176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:22,355] [INFO] GTDB search result was written to GCF_003385715.1_ASM338571v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:22,356] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:22,360] [INFO] DFAST_QC result json was written to GCF_003385715.1_ASM338571v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:22,360] [INFO] DFAST_QC completed!
[2024-01-25 17:35:22,360] [INFO] Total running time: 0h1m15s