[2024-01-24 13:28:54,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:54,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:54,906] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6fe1a8d-5c9d-49a2-bb76-23404e9387af/dqc_reference
[2024-01-24 13:28:56,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:56,152] [INFO] Task started: Prodigal
[2024-01-24 13:28:56,153] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b12d6de-ffbc-405e-a969-213026004b29/GCF_019966535.1_ASM1996653v1_genomic.fna.gz | prodigal -d GCF_019966535.1_ASM1996653v1_genomic.fna/cds.fna -a GCF_019966535.1_ASM1996653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:29:15,291] [INFO] Task succeeded: Prodigal
[2024-01-24 13:29:15,291] [INFO] Task started: HMMsearch
[2024-01-24 13:29:15,291] [INFO] Running command: hmmsearch --tblout GCF_019966535.1_ASM1996653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6fe1a8d-5c9d-49a2-bb76-23404e9387af/dqc_reference/reference_markers.hmm GCF_019966535.1_ASM1996653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:29:15,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:29:15,613] [INFO] Found 6/6 markers.
[2024-01-24 13:29:15,672] [INFO] Query marker FASTA was written to GCF_019966535.1_ASM1996653v1_genomic.fna/markers.fasta
[2024-01-24 13:29:15,673] [INFO] Task started: Blastn
[2024-01-24 13:29:15,673] [INFO] Running command: blastn -query GCF_019966535.1_ASM1996653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6fe1a8d-5c9d-49a2-bb76-23404e9387af/dqc_reference/reference_markers.fasta -out GCF_019966535.1_ASM1996653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:16,693] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:16,697] [INFO] Selected 26 target genomes.
[2024-01-24 13:29:16,697] [INFO] Target genome list was writen to GCF_019966535.1_ASM1996653v1_genomic.fna/target_genomes.txt
[2024-01-24 13:29:16,746] [INFO] Task started: fastANI
[2024-01-24 13:29:16,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b12d6de-ffbc-405e-a969-213026004b29/GCF_019966535.1_ASM1996653v1_genomic.fna.gz --refList GCF_019966535.1_ASM1996653v1_genomic.fna/target_genomes.txt --output GCF_019966535.1_ASM1996653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:42,229] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:42,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6fe1a8d-5c9d-49a2-bb76-23404e9387af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:42,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6fe1a8d-5c9d-49a2-bb76-23404e9387af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:42,254] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:29:42,254] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:29:42,255] [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
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	80.0351	788	1965	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.9678	746	1965	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.8676	713	1965	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.7572	697	1965	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	79.5708	740	1965	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	79.5676	731	1965	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.4988	599	1965	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.4398	722	1965	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	79.4003	672	1965	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	79.3654	665	1965	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.1819	651	1965	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	79.1368	653	1965	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.0136	657	1965	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	79.0108	527	1965	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.9337	493	1965	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	78.8793	570	1965	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.7412	567	1965	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.6136	546	1965	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.5815	538	1965	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	78.5753	535	1965	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	78.4809	553	1965	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	78.4127	402	1965	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	78.3952	437	1965	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.2858	493	1965	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	78.1034	437	1965	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.0728	487	1965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:42,256] [INFO] DFAST Taxonomy check result was written to GCF_019966535.1_ASM1996653v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:42,257] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:42,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:42,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6fe1a8d-5c9d-49a2-bb76-23404e9387af/dqc_reference/checkm_data
[2024-01-24 13:29:42,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:42,314] [INFO] Task started: CheckM
[2024-01-24 13:29:42,314] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019966535.1_ASM1996653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019966535.1_ASM1996653v1_genomic.fna/checkm_input GCF_019966535.1_ASM1996653v1_genomic.fna/checkm_result
[2024-01-24 13:30:43,463] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:43,464] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:43,489] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:43,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:43,489] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019966535.1_ASM1996653v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:43,490] [INFO] Task started: Blastn
[2024-01-24 13:30:43,490] [INFO] Running command: blastn -query GCF_019966535.1_ASM1996653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6fe1a8d-5c9d-49a2-bb76-23404e9387af/dqc_reference/reference_markers_gtdb.fasta -out GCF_019966535.1_ASM1996653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:45,192] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:45,197] [INFO] Selected 28 target genomes.
[2024-01-24 13:30:45,197] [INFO] Target genome list was writen to GCF_019966535.1_ASM1996653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:45,229] [INFO] Task started: fastANI
[2024-01-24 13:30:45,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b12d6de-ffbc-405e-a969-213026004b29/GCF_019966535.1_ASM1996653v1_genomic.fna.gz --refList GCF_019966535.1_ASM1996653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019966535.1_ASM1996653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:10,961] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:10,987] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:31:10,987] [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_009789075.1	s__Pseudooceanicola pacificus	81.2737	533	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	80.3929	725	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	80.0783	761	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	80.0323	725	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000153725.1	s__Salipiger bermudensis	79.9992	740	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_900102075.1	s__Salipiger thiooxidans	79.991	793	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_001969385.1	s__Salipiger profundus	79.8815	712	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_003344785.1	s__Puniceibacterium profundi	79.8475	753	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	79.8436	715	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	79.7707	700	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	79.6995	724	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.6473	744	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	79.6093	726	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900109035.1	s__Cribrihabitans marinus	79.5795	659	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	79.3289	632	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.2933	628	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	79.2486	560	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_900129345.1	s__Ruegeria intermedia	79.2206	565	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762635.1	s__JABURR01 sp014762635	79.1079	521	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABURR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	79.0134	557	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	78.9852	542	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.7749	562	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	78.6945	565	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.5962	536	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923445.1	s__Puniceibacterium confluentis	78.5623	537	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115815.1	s__Roseivivax halotolerans	78.3931	438	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.75	97.75	0.88	0.88	2	-
GCF_900188035.1	s__Puniceibacterium sediminis	78.0952	438	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995245.1	s__Tateyamaria sp007995245	78.0412	409	1965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:10,989] [INFO] GTDB search result was written to GCF_019966535.1_ASM1996653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:10,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:10,995] [INFO] DFAST_QC result json was written to GCF_019966535.1_ASM1996653v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:10,995] [INFO] DFAST_QC completed!
[2024-01-24 13:31:10,995] [INFO] Total running time: 0h2m16s