[2023-06-04 19:51:33,957] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:51:33,969] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:51:33,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg7939b6e3-64b8-4f26-b015-43d5d4ebb1cb/dqc_reference
[2023-06-04 19:51:36,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:51:36,302] [INFO] Task started: Prodigal
[2023-06-04 19:51:36,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg30527900-e60d-4e67-ad4d-4dc789e8ae22/GCA_004562055.1_ASM456205v1_genomic.fna.gz | prodigal -d GCA_004562055.1_ASM456205v1_genomic.fna/cds.fna -a GCA_004562055.1_ASM456205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:51:52,304] [INFO] Task succeeded: Prodigal
[2023-06-04 19:51:52,305] [INFO] Task started: HMMsearch
[2023-06-04 19:51:52,305] [INFO] Running command: hmmsearch --tblout GCA_004562055.1_ASM456205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7939b6e3-64b8-4f26-b015-43d5d4ebb1cb/dqc_reference/reference_markers.hmm GCA_004562055.1_ASM456205v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:51:52,553] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:51:52,556] [INFO] Found 6/6 markers.
[2023-06-04 19:51:52,590] [INFO] Query marker FASTA was written to GCA_004562055.1_ASM456205v1_genomic.fna/markers.fasta
[2023-06-04 19:51:52,591] [INFO] Task started: Blastn
[2023-06-04 19:51:52,591] [INFO] Running command: blastn -query GCA_004562055.1_ASM456205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7939b6e3-64b8-4f26-b015-43d5d4ebb1cb/dqc_reference/reference_markers.fasta -out GCA_004562055.1_ASM456205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:51:53,155] [INFO] Task succeeded: Blastn
[2023-06-04 19:51:53,159] [INFO] Selected 20 target genomes.
[2023-06-04 19:51:53,160] [INFO] Target genome list was writen to GCA_004562055.1_ASM456205v1_genomic.fna/target_genomes.txt
[2023-06-04 19:51:53,191] [INFO] Task started: fastANI
[2023-06-04 19:51:53,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg30527900-e60d-4e67-ad4d-4dc789e8ae22/GCA_004562055.1_ASM456205v1_genomic.fna.gz --refList GCA_004562055.1_ASM456205v1_genomic.fna/target_genomes.txt --output GCA_004562055.1_ASM456205v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:52:04,861] [INFO] Task succeeded: fastANI
[2023-06-04 19:52:04,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7939b6e3-64b8-4f26-b015-43d5d4ebb1cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:52:04,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7939b6e3-64b8-4f26-b015-43d5d4ebb1cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:52:04,866] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:52:04,866] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 19:52:04,866] [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
--------------------------------------------------------------------------------
[2023-06-04 19:52:04,869] [INFO] DFAST Taxonomy check result was written to GCA_004562055.1_ASM456205v1_genomic.fna/tc_result.tsv
[2023-06-04 19:52:04,870] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:52:04,871] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:52:04,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7939b6e3-64b8-4f26-b015-43d5d4ebb1cb/dqc_reference/checkm_data
[2023-06-04 19:52:04,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:52:04,922] [INFO] Task started: CheckM
[2023-06-04 19:52:04,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004562055.1_ASM456205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004562055.1_ASM456205v1_genomic.fna/checkm_input GCA_004562055.1_ASM456205v1_genomic.fna/checkm_result
[2023-06-04 19:52:53,625] [INFO] Task succeeded: CheckM
[2023-06-04 19:52:53,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 12.50%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-04 19:52:53,653] [INFO] ===== Completeness check finished =====
[2023-06-04 19:52:53,653] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:52:53,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004562055.1_ASM456205v1_genomic.fna/markers.fasta)
[2023-06-04 19:52:53,654] [INFO] Task started: Blastn
[2023-06-04 19:52:53,654] [INFO] Running command: blastn -query GCA_004562055.1_ASM456205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7939b6e3-64b8-4f26-b015-43d5d4ebb1cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_004562055.1_ASM456205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:52:54,399] [INFO] Task succeeded: Blastn
[2023-06-04 19:52:54,404] [INFO] Selected 17 target genomes.
[2023-06-04 19:52:54,404] [INFO] Target genome list was writen to GCA_004562055.1_ASM456205v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:52:54,417] [INFO] Task started: fastANI
[2023-06-04 19:52:54,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg30527900-e60d-4e67-ad4d-4dc789e8ae22/GCA_004562055.1_ASM456205v1_genomic.fna.gz --refList GCA_004562055.1_ASM456205v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004562055.1_ASM456205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:53:01,024] [INFO] Task succeeded: fastANI
[2023-06-04 19:53:01,040] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:53:01,040] [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_900546925.1	s__Cryptobacteroides sp900546925	98.7599	524	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.81	98.70	0.85	0.79	6	conclusive
GCA_000435075.1	s__Cryptobacteroides sp000435075	81.1437	252	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.30	97.06	0.87	0.85	4	-
GCA_000434935.1	s__Cryptobacteroides sp000434935	79.7386	250	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.20	96.88	0.85	0.83	4	-
GCA_000432515.1	s__Cryptobacteroides sp000432515	79.0888	242	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.23	97.18	0.82	0.82	4	-
GCA_004552615.1	s__Cryptobacteroides sp004552615	78.4773	113	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.38	98.38	0.80	0.80	2	-
GCA_900769145.1	s__Cryptobacteroides sp900769145	77.879	118	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900167925.1	s__Cryptobacteroides sp900167925	77.5145	78	917	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.91	97.12	0.93	0.91	9	-
--------------------------------------------------------------------------------
[2023-06-04 19:53:01,043] [INFO] GTDB search result was written to GCA_004562055.1_ASM456205v1_genomic.fna/result_gtdb.tsv
[2023-06-04 19:53:01,043] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:53:01,046] [INFO] DFAST_QC result json was written to GCA_004562055.1_ASM456205v1_genomic.fna/dqc_result.json
[2023-06-04 19:53:01,046] [INFO] DFAST_QC completed!
[2023-06-04 19:53:01,046] [INFO] Total running time: 0h1m27s