[2024-01-24 14:46:35,700] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:35,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:35,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9d904a5-7e94-4dbb-9ca1-cc40cd931fb7/dqc_reference
[2024-01-24 14:46:37,184] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:37,185] [INFO] Task started: Prodigal
[2024-01-24 14:46:37,185] [INFO] Running command: gunzip -c /var/lib/cwl/stgbda3c751-7659-4205-a1d4-61e4329dee92/GCF_005938215.1_ASM593821v1_genomic.fna.gz | prodigal -d GCF_005938215.1_ASM593821v1_genomic.fna/cds.fna -a GCF_005938215.1_ASM593821v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:49,692] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:49,693] [INFO] Task started: HMMsearch
[2024-01-24 14:46:49,693] [INFO] Running command: hmmsearch --tblout GCF_005938215.1_ASM593821v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9d904a5-7e94-4dbb-9ca1-cc40cd931fb7/dqc_reference/reference_markers.hmm GCF_005938215.1_ASM593821v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:49,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:49,912] [INFO] Found 6/6 markers.
[2024-01-24 14:46:49,947] [INFO] Query marker FASTA was written to GCF_005938215.1_ASM593821v1_genomic.fna/markers.fasta
[2024-01-24 14:46:49,948] [INFO] Task started: Blastn
[2024-01-24 14:46:49,948] [INFO] Running command: blastn -query GCF_005938215.1_ASM593821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d904a5-7e94-4dbb-9ca1-cc40cd931fb7/dqc_reference/reference_markers.fasta -out GCF_005938215.1_ASM593821v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:50,972] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:50,976] [INFO] Selected 15 target genomes.
[2024-01-24 14:46:50,976] [INFO] Target genome list was writen to GCF_005938215.1_ASM593821v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:50,982] [INFO] Task started: fastANI
[2024-01-24 14:46:50,983] [INFO] Running command: fastANI --query /var/lib/cwl/stgbda3c751-7659-4205-a1d4-61e4329dee92/GCF_005938215.1_ASM593821v1_genomic.fna.gz --refList GCF_005938215.1_ASM593821v1_genomic.fna/target_genomes.txt --output GCF_005938215.1_ASM593821v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:03,016] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:03,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9d904a5-7e94-4dbb-9ca1-cc40cd931fb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:03,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9d904a5-7e94-4dbb-9ca1-cc40cd931fb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:03,028] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:03,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:03,029] [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
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	100.0	1401	1401	95	conclusive
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	84.3419	964	1401	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	82.5408	786	1401	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	81.2316	720	1401	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	81.1722	714	1401	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	81.164	793	1401	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	80.97	792	1401	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	80.1914	660	1401	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	79.8909	657	1401	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	78.9531	518	1401	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.5772	420	1401	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.4834	359	1401	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.2369	385	1401	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.8659	335	1401	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8497	348	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:03,030] [INFO] DFAST Taxonomy check result was written to GCF_005938215.1_ASM593821v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:03,031] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:03,031] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:03,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9d904a5-7e94-4dbb-9ca1-cc40cd931fb7/dqc_reference/checkm_data
[2024-01-24 14:47:03,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:03,071] [INFO] Task started: CheckM
[2024-01-24 14:47:03,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005938215.1_ASM593821v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005938215.1_ASM593821v1_genomic.fna/checkm_input GCF_005938215.1_ASM593821v1_genomic.fna/checkm_result
[2024-01-24 14:47:42,308] [INFO] Task succeeded: CheckM
[2024-01-24 14:47:42,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:47:42,327] [INFO] ===== Completeness check finished =====
[2024-01-24 14:47:42,327] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:47:42,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005938215.1_ASM593821v1_genomic.fna/markers.fasta)
[2024-01-24 14:47:42,327] [INFO] Task started: Blastn
[2024-01-24 14:47:42,328] [INFO] Running command: blastn -query GCF_005938215.1_ASM593821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d904a5-7e94-4dbb-9ca1-cc40cd931fb7/dqc_reference/reference_markers_gtdb.fasta -out GCF_005938215.1_ASM593821v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:44,318] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:44,321] [INFO] Selected 11 target genomes.
[2024-01-24 14:47:44,321] [INFO] Target genome list was writen to GCF_005938215.1_ASM593821v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:47:44,329] [INFO] Task started: fastANI
[2024-01-24 14:47:44,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgbda3c751-7659-4205-a1d4-61e4329dee92/GCF_005938215.1_ASM593821v1_genomic.fna.gz --refList GCF_005938215.1_ASM593821v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005938215.1_ASM593821v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:47:54,341] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:54,353] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:47:54,353] [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_005938215.1	s__Ruegeria sediminis	100.0	1401	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001507595.1	s__Ruegeria marisrubri	84.3451	964	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	82.5439	786	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	82.2474	758	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_013031405.1	s__Ruegeria sp013031405	82.0988	869	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	81.3676	766	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_900109035.1	s__Cribrihabitans marinus	81.216	721	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010500245.1	s__Ruegeria_B sp010500245	80.8013	758	1401	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_013031355.1	s__Ruegeria arenilitoris_C	80.2281	692	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_013032025.1	s__Ruegeria atlantica_C	79.9324	639	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009363615.1	s__Ruegeria sp009363615	79.7731	627	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
--------------------------------------------------------------------------------
[2024-01-24 14:47:54,354] [INFO] GTDB search result was written to GCF_005938215.1_ASM593821v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:47:54,355] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:47:54,359] [INFO] DFAST_QC result json was written to GCF_005938215.1_ASM593821v1_genomic.fna/dqc_result.json
[2024-01-24 14:47:54,359] [INFO] DFAST_QC completed!
[2024-01-24 14:47:54,359] [INFO] Total running time: 0h1m19s