[2024-01-24 12:05:58,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:58,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:58,209] [INFO] DQC Reference Directory: /var/lib/cwl/stgea1cc45f-4016-4152-a337-34f353929575/dqc_reference
[2024-01-24 12:05:59,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:59,534] [INFO] Task started: Prodigal
[2024-01-24 12:05:59,534] [INFO] Running command: gunzip -c /var/lib/cwl/stg75aa7e73-d057-47da-bb41-343ae307196a/GCF_004000255.1_ASM400025v1_genomic.fna.gz | prodigal -d GCF_004000255.1_ASM400025v1_genomic.fna/cds.fna -a GCF_004000255.1_ASM400025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:14,219] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:14,219] [INFO] Task started: HMMsearch
[2024-01-24 12:06:14,220] [INFO] Running command: hmmsearch --tblout GCF_004000255.1_ASM400025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea1cc45f-4016-4152-a337-34f353929575/dqc_reference/reference_markers.hmm GCF_004000255.1_ASM400025v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:14,550] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:14,551] [INFO] Found 6/6 markers.
[2024-01-24 12:06:14,596] [INFO] Query marker FASTA was written to GCF_004000255.1_ASM400025v1_genomic.fna/markers.fasta
[2024-01-24 12:06:14,597] [INFO] Task started: Blastn
[2024-01-24 12:06:14,597] [INFO] Running command: blastn -query GCF_004000255.1_ASM400025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea1cc45f-4016-4152-a337-34f353929575/dqc_reference/reference_markers.fasta -out GCF_004000255.1_ASM400025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:15,600] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:15,605] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:15,605] [INFO] Target genome list was writen to GCF_004000255.1_ASM400025v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:15,610] [INFO] Task started: fastANI
[2024-01-24 12:06:15,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg75aa7e73-d057-47da-bb41-343ae307196a/GCF_004000255.1_ASM400025v1_genomic.fna.gz --refList GCF_004000255.1_ASM400025v1_genomic.fna/target_genomes.txt --output GCF_004000255.1_ASM400025v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:29,962] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:29,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea1cc45f-4016-4152-a337-34f353929575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:29,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea1cc45f-4016-4152-a337-34f353929575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:29,979] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:29,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:29,980] [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
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	100.0	1502	1504	95	conclusive
Nioella sediminis	strain=JS7-11	GCA_001879695.1	1912092	1912092	type	True	92.1633	1132	1504	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	81.9857	878	1504	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.716	513	1504	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.6691	521	1504	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.5619	375	1504	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5217	422	1504	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.5195	421	1504	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	78.3899	483	1504	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	78.2533	417	1504	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.0637	425	1504	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.057	406	1504	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.0373	426	1504	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.8531	363	1504	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.8117	358	1504	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	77.7836	357	1504	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	77.4903	345	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:29,982] [INFO] DFAST Taxonomy check result was written to GCF_004000255.1_ASM400025v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:29,983] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:29,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:29,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea1cc45f-4016-4152-a337-34f353929575/dqc_reference/checkm_data
[2024-01-24 12:06:29,985] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:30,031] [INFO] Task started: CheckM
[2024-01-24 12:06:30,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004000255.1_ASM400025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004000255.1_ASM400025v1_genomic.fna/checkm_input GCF_004000255.1_ASM400025v1_genomic.fna/checkm_result
[2024-01-24 12:07:16,131] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:16,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:16,178] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:16,178] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:16,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004000255.1_ASM400025v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:16,179] [INFO] Task started: Blastn
[2024-01-24 12:07:16,179] [INFO] Running command: blastn -query GCF_004000255.1_ASM400025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea1cc45f-4016-4152-a337-34f353929575/dqc_reference/reference_markers_gtdb.fasta -out GCF_004000255.1_ASM400025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:17,979] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:17,984] [INFO] Selected 9 target genomes.
[2024-01-24 12:07:17,985] [INFO] Target genome list was writen to GCF_004000255.1_ASM400025v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:17,991] [INFO] Task started: fastANI
[2024-01-24 12:07:17,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg75aa7e73-d057-47da-bb41-343ae307196a/GCF_004000255.1_ASM400025v1_genomic.fna.gz --refList GCF_004000255.1_ASM400025v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004000255.1_ASM400025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:26,350] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:26,361] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:26,362] [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_004000255.1	s__Nioella ostreopsis	100.0	1502	1504	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001879695.1	s__Nioella sediminis	92.1516	1133	1504	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001879715.1	s__Nioella nitratireducens	81.9945	876	1504	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003428585.1	s__Nioella sp003428585	81.3337	770	1504	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783145.1	s__Nioella sp002783145	81.1023	589	1504	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nioella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155465.1	s__Alterinioella nitratireducens	80.673	790	1504	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.8796	525	1504	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	78.7001	515	1504	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	77.9521	413	1504	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:26,363] [INFO] GTDB search result was written to GCF_004000255.1_ASM400025v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:26,364] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:26,369] [INFO] DFAST_QC result json was written to GCF_004000255.1_ASM400025v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:26,370] [INFO] DFAST_QC completed!
[2024-01-24 12:07:26,370] [INFO] Total running time: 0h1m28s