[2024-01-24 14:50:03,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:50:03,950] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:50:03,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg5314e4b9-c127-426f-aec1-a269b87acbe6/dqc_reference
[2024-01-24 14:50:05,330] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:50:05,331] [INFO] Task started: Prodigal
[2024-01-24 14:50:05,331] [INFO] Running command: gunzip -c /var/lib/cwl/stge3dab6b0-4d56-4b92-848e-526054236ce2/GCF_002075285.3_ASM207528v3_genomic.fna.gz | prodigal -d GCF_002075285.3_ASM207528v3_genomic.fna/cds.fna -a GCF_002075285.3_ASM207528v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:50:20,785] [INFO] Task succeeded: Prodigal
[2024-01-24 14:50:20,786] [INFO] Task started: HMMsearch
[2024-01-24 14:50:20,786] [INFO] Running command: hmmsearch --tblout GCF_002075285.3_ASM207528v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5314e4b9-c127-426f-aec1-a269b87acbe6/dqc_reference/reference_markers.hmm GCF_002075285.3_ASM207528v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:50:21,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:50:21,124] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge3dab6b0-4d56-4b92-848e-526054236ce2/GCF_002075285.3_ASM207528v3_genomic.fna.gz]
[2024-01-24 14:50:21,177] [INFO] Query marker FASTA was written to GCF_002075285.3_ASM207528v3_genomic.fna/markers.fasta
[2024-01-24 14:50:21,177] [INFO] Task started: Blastn
[2024-01-24 14:50:21,177] [INFO] Running command: blastn -query GCF_002075285.3_ASM207528v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg5314e4b9-c127-426f-aec1-a269b87acbe6/dqc_reference/reference_markers.fasta -out GCF_002075285.3_ASM207528v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:21,788] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:21,791] [INFO] Selected 16 target genomes.
[2024-01-24 14:50:21,792] [INFO] Target genome list was writen to GCF_002075285.3_ASM207528v3_genomic.fna/target_genomes.txt
[2024-01-24 14:50:21,799] [INFO] Task started: fastANI
[2024-01-24 14:50:21,800] [INFO] Running command: fastANI --query /var/lib/cwl/stge3dab6b0-4d56-4b92-848e-526054236ce2/GCF_002075285.3_ASM207528v3_genomic.fna.gz --refList GCF_002075285.3_ASM207528v3_genomic.fna/target_genomes.txt --output GCF_002075285.3_ASM207528v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:50:35,877] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:35,878] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5314e4b9-c127-426f-aec1-a269b87acbe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:50:35,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5314e4b9-c127-426f-aec1-a269b87acbe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:50:35,883] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:50:35,884] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:50:35,884] [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
Halomicronema hongdechloris	strain=C2206	GCA_002075285.3	1209493	1209493	type	True	100.0	1858	1859	95	conclusive
Acaryochloris marina	strain=MBIC11017	GCA_000018105.1	155978	155978	type	True	76.3584	57	1859	95	below_threshold
Adonisia turfae	strain=CCMR0081	GCA_011009555.1	2950184	2950184	type	True	76.0939	84	1859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:50:35,886] [INFO] DFAST Taxonomy check result was written to GCF_002075285.3_ASM207528v3_genomic.fna/tc_result.tsv
[2024-01-24 14:50:35,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:50:35,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:50:35,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5314e4b9-c127-426f-aec1-a269b87acbe6/dqc_reference/checkm_data
[2024-01-24 14:50:35,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:50:35,944] [INFO] Task started: CheckM
[2024-01-24 14:50:35,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002075285.3_ASM207528v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002075285.3_ASM207528v3_genomic.fna/checkm_input GCF_002075285.3_ASM207528v3_genomic.fna/checkm_result
[2024-01-24 14:51:23,539] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:23,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:23,562] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:23,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:23,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002075285.3_ASM207528v3_genomic.fna/markers.fasta)
[2024-01-24 14:51:23,563] [INFO] Task started: Blastn
[2024-01-24 14:51:23,564] [INFO] Running command: blastn -query GCF_002075285.3_ASM207528v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg5314e4b9-c127-426f-aec1-a269b87acbe6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002075285.3_ASM207528v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:24,394] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:24,397] [INFO] Selected 22 target genomes.
[2024-01-24 14:51:24,397] [INFO] Target genome list was writen to GCF_002075285.3_ASM207528v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:24,414] [INFO] Task started: fastANI
[2024-01-24 14:51:24,414] [INFO] Running command: fastANI --query /var/lib/cwl/stge3dab6b0-4d56-4b92-848e-526054236ce2/GCF_002075285.3_ASM207528v3_genomic.fna.gz --refList GCF_002075285.3_ASM207528v3_genomic.fna/target_genomes_gtdb.txt --output GCF_002075285.3_ASM207528v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:45,140] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:45,156] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:45,156] [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_002075285.3	s__Halomicronema_B hongdechloris	100.0	1859	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Halomicronema_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000309385.1	s__Nodosilinea nodulosa	76.9764	177	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970085.1	s__Nodosilinea sp018970085	76.6719	80	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031045.1	s__Nodosilinea sp012031045	76.5701	110	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696675.1	s__Nodosilinea tenue	76.5588	150	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016888135.1	s__RECH01 sp016888135	76.5392	83	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__RECH01	95.0	96.61	96.61	0.91	0.91	3	-
GCF_015207525.1	s__Nodosilinea sp015207525	76.468	146	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763385.1	s__Nodosilinea sp000763385	76.3779	180	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911975.1	s__Nodosilinea sp003564835	76.3174	173	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.57	99.57	0.98	0.98	2	-
GCA_003017855.1	s__Nodosilinea sp003017855	76.2828	153	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.92	99.92	0.94	0.94	2	-
GCF_014695775.1	s__Nodosilinea sp014695775	76.2606	122	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	100.00	99.99	0.99	0.99	3	-
GCF_014695395.1	s__Nodosilinea sp014695395	76.1476	129	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207365.1	s__FACHB-8 sp015207365	75.8666	70	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__FACHB-8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696715.1	s__JACVSF01 sp014534085	75.68	156	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__JACVSF01	95.0	96.97	96.97	0.97	0.97	2	-
GCA_007135385.1	s__Nodosilinea sp007135385	75.57	95	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	99.71	99.33	0.94	0.89	7	-
GCA_014534385.1	s__JACVSF01 sp014534385	75.5377	89	1859	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__JACVSF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:45,157] [INFO] GTDB search result was written to GCF_002075285.3_ASM207528v3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:45,158] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:45,161] [INFO] DFAST_QC result json was written to GCF_002075285.3_ASM207528v3_genomic.fna/dqc_result.json
[2024-01-24 14:51:45,161] [INFO] DFAST_QC completed!
[2024-01-24 14:51:45,161] [INFO] Total running time: 0h1m41s