[2023-06-16 19:10:37,489] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:10:37,491] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:10:37,491] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0c01c5b-31ac-49fd-a0bc-c0f87869956e/dqc_reference
[2023-06-16 19:10:38,613] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:10:38,614] [INFO] Task started: Prodigal
[2023-06-16 19:10:38,614] [INFO] Running command: gunzip -c /var/lib/cwl/stgfaf2abf9-edf9-4336-a07e-89772f6a7ecc/GCA_003672115.1_ASM367211v1_genomic.fna.gz | prodigal -d GCA_003672115.1_ASM367211v1_genomic.fna/cds.fna -a GCA_003672115.1_ASM367211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:10:42,035] [INFO] Task succeeded: Prodigal
[2023-06-16 19:10:42,035] [INFO] Task started: HMMsearch
[2023-06-16 19:10:42,036] [INFO] Running command: hmmsearch --tblout GCA_003672115.1_ASM367211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0c01c5b-31ac-49fd-a0bc-c0f87869956e/dqc_reference/reference_markers.hmm GCA_003672115.1_ASM367211v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:10:42,214] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:10:42,215] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfaf2abf9-edf9-4336-a07e-89772f6a7ecc/GCA_003672115.1_ASM367211v1_genomic.fna.gz]
[2023-06-16 19:10:42,238] [INFO] Query marker FASTA was written to GCA_003672115.1_ASM367211v1_genomic.fna/markers.fasta
[2023-06-16 19:10:42,239] [INFO] Task started: Blastn
[2023-06-16 19:10:42,239] [INFO] Running command: blastn -query GCA_003672115.1_ASM367211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c01c5b-31ac-49fd-a0bc-c0f87869956e/dqc_reference/reference_markers.fasta -out GCA_003672115.1_ASM367211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:10:42,701] [INFO] Task succeeded: Blastn
[2023-06-16 19:10:42,704] [INFO] Selected 5 target genomes.
[2023-06-16 19:10:42,705] [INFO] Target genome list was writen to GCA_003672115.1_ASM367211v1_genomic.fna/target_genomes.txt
[2023-06-16 19:10:42,707] [INFO] Task started: fastANI
[2023-06-16 19:10:42,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaf2abf9-edf9-4336-a07e-89772f6a7ecc/GCA_003672115.1_ASM367211v1_genomic.fna.gz --refList GCA_003672115.1_ASM367211v1_genomic.fna/target_genomes.txt --output GCA_003672115.1_ASM367211v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:10:44,411] [INFO] Task succeeded: fastANI
[2023-06-16 19:10:44,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0c01c5b-31ac-49fd-a0bc-c0f87869956e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:10:44,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0c01c5b-31ac-49fd-a0bc-c0f87869956e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:10:44,413] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:10:44,413] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 19:10:44,413] [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
--------------------------------------------------------------------------------
[2023-06-16 19:10:44,415] [INFO] DFAST Taxonomy check result was written to GCA_003672115.1_ASM367211v1_genomic.fna/tc_result.tsv
[2023-06-16 19:10:44,416] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:10:44,416] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:10:44,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0c01c5b-31ac-49fd-a0bc-c0f87869956e/dqc_reference/checkm_data
[2023-06-16 19:10:44,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:10:44,439] [INFO] Task started: CheckM
[2023-06-16 19:10:44,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003672115.1_ASM367211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003672115.1_ASM367211v1_genomic.fna/checkm_input GCA_003672115.1_ASM367211v1_genomic.fna/checkm_result
[2023-06-16 19:11:01,025] [INFO] Task succeeded: CheckM
[2023-06-16 19:11:01,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.06%
Contamintation: 2.95%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-16 19:11:01,043] [INFO] ===== Completeness check finished =====
[2023-06-16 19:11:01,044] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:11:01,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003672115.1_ASM367211v1_genomic.fna/markers.fasta)
[2023-06-16 19:11:01,045] [INFO] Task started: Blastn
[2023-06-16 19:11:01,045] [INFO] Running command: blastn -query GCA_003672115.1_ASM367211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0c01c5b-31ac-49fd-a0bc-c0f87869956e/dqc_reference/reference_markers_gtdb.fasta -out GCA_003672115.1_ASM367211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:01,502] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:01,506] [INFO] Selected 9 target genomes.
[2023-06-16 19:11:01,506] [INFO] Target genome list was writen to GCA_003672115.1_ASM367211v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:11:01,528] [INFO] Task started: fastANI
[2023-06-16 19:11:01,529] [INFO] Running command: fastANI --query /var/lib/cwl/stgfaf2abf9-edf9-4336-a07e-89772f6a7ecc/GCA_003672115.1_ASM367211v1_genomic.fna.gz --refList GCA_003672115.1_ASM367211v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003672115.1_ASM367211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:11:04,185] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:04,192] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:11:04,192] [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
GCA_013330015.1	s__MGIIa-L2 sp8574u	98.3533	217	353	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	100.00	100.00	0.98	0.98	2	conclusive
GCA_018623995.1	s__MGIIa-L2 sp018623995	89.6454	251	353	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692685.1	s__MGIIa-L2 sp002692685	88.8671	191	353	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270265.1	s__MGIIa-L2 sp012270265	88.7611	235	353	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722615.1	s__MGIIa-L2 sp002722615	79.8726	153	353	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	-
GCA_013911465.1	s__MGIIa-L2 sp013911465	79.4108	132	353	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706065.1	s__MGIIa-L2 sp002706065	78.6026	160	353	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666575.1	s__MGIIa-L2 sp018666575	77.1119	71	353	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.20	99.20	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-16 19:11:04,194] [INFO] GTDB search result was written to GCA_003672115.1_ASM367211v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:11:04,194] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:11:04,197] [INFO] DFAST_QC result json was written to GCA_003672115.1_ASM367211v1_genomic.fna/dqc_result.json
[2023-06-16 19:11:04,197] [INFO] DFAST_QC completed!
[2023-06-16 19:11:04,197] [INFO] Total running time: 0h0m27s