[2023-06-29 22:57:25,865] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:57:25,868] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:57:25,868] [INFO] DQC Reference Directory: /var/lib/cwl/stgfebdb823-e46f-4c6a-a1aa-9c5faf05ba93/dqc_reference
[2023-06-29 22:57:27,108] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:57:27,109] [INFO] Task started: Prodigal
[2023-06-29 22:57:27,109] [INFO] Running command: gunzip -c /var/lib/cwl/stge045da37-aac8-4105-ab0e-c09342e7bcef/GCA_016710265.1_ASM1671026v1_genomic.fna.gz | prodigal -d GCA_016710265.1_ASM1671026v1_genomic.fna/cds.fna -a GCA_016710265.1_ASM1671026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:57:45,016] [INFO] Task succeeded: Prodigal
[2023-06-29 22:57:45,017] [INFO] Task started: HMMsearch
[2023-06-29 22:57:45,017] [INFO] Running command: hmmsearch --tblout GCA_016710265.1_ASM1671026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfebdb823-e46f-4c6a-a1aa-9c5faf05ba93/dqc_reference/reference_markers.hmm GCA_016710265.1_ASM1671026v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:57:45,280] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:57:45,282] [INFO] Found 6/6 markers.
[2023-06-29 22:57:45,321] [INFO] Query marker FASTA was written to GCA_016710265.1_ASM1671026v1_genomic.fna/markers.fasta
[2023-06-29 22:57:45,322] [INFO] Task started: Blastn
[2023-06-29 22:57:45,322] [INFO] Running command: blastn -query GCA_016710265.1_ASM1671026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfebdb823-e46f-4c6a-a1aa-9c5faf05ba93/dqc_reference/reference_markers.fasta -out GCA_016710265.1_ASM1671026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:57:45,937] [INFO] Task succeeded: Blastn
[2023-06-29 22:57:45,943] [INFO] Selected 27 target genomes.
[2023-06-29 22:57:45,944] [INFO] Target genome list was writen to GCA_016710265.1_ASM1671026v1_genomic.fna/target_genomes.txt
[2023-06-29 22:57:45,949] [INFO] Task started: fastANI
[2023-06-29 22:57:45,949] [INFO] Running command: fastANI --query /var/lib/cwl/stge045da37-aac8-4105-ab0e-c09342e7bcef/GCA_016710265.1_ASM1671026v1_genomic.fna.gz --refList GCA_016710265.1_ASM1671026v1_genomic.fna/target_genomes.txt --output GCA_016710265.1_ASM1671026v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:58:02,978] [INFO] Task succeeded: fastANI
[2023-06-29 22:58:02,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfebdb823-e46f-4c6a-a1aa-9c5faf05ba93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:58:02,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfebdb823-e46f-4c6a-a1aa-9c5faf05ba93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:58:02,982] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:58:02,982] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:58:02,982] [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
--------------------------------------------------------------------------------
[2023-06-29 22:58:02,984] [INFO] DFAST Taxonomy check result was written to GCA_016710265.1_ASM1671026v1_genomic.fna/tc_result.tsv
[2023-06-29 22:58:02,985] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:58:02,985] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:58:02,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfebdb823-e46f-4c6a-a1aa-9c5faf05ba93/dqc_reference/checkm_data
[2023-06-29 22:58:02,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:58:03,031] [INFO] Task started: CheckM
[2023-06-29 22:58:03,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016710265.1_ASM1671026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016710265.1_ASM1671026v1_genomic.fna/checkm_input GCA_016710265.1_ASM1671026v1_genomic.fna/checkm_result
[2023-06-29 22:58:56,813] [INFO] Task succeeded: CheckM
[2023-06-29 22:58:56,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:58:56,834] [INFO] ===== Completeness check finished =====
[2023-06-29 22:58:56,834] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:58:56,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016710265.1_ASM1671026v1_genomic.fna/markers.fasta)
[2023-06-29 22:58:56,835] [INFO] Task started: Blastn
[2023-06-29 22:58:56,835] [INFO] Running command: blastn -query GCA_016710265.1_ASM1671026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfebdb823-e46f-4c6a-a1aa-9c5faf05ba93/dqc_reference/reference_markers_gtdb.fasta -out GCA_016710265.1_ASM1671026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:58:57,575] [INFO] Task succeeded: Blastn
[2023-06-29 22:58:57,580] [INFO] Selected 26 target genomes.
[2023-06-29 22:58:57,580] [INFO] Target genome list was writen to GCA_016710265.1_ASM1671026v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:58:57,590] [INFO] Task started: fastANI
[2023-06-29 22:58:57,590] [INFO] Running command: fastANI --query /var/lib/cwl/stge045da37-aac8-4105-ab0e-c09342e7bcef/GCA_016710265.1_ASM1671026v1_genomic.fna.gz --refList GCA_016710265.1_ASM1671026v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016710265.1_ASM1671026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:59:14,545] [INFO] Task succeeded: fastANI
[2023-06-29 22:59:14,559] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:59:14,559] [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_016710265.1	s__UBA3362 sp016710265	100.0	1338	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA3362	95.0	99.12	98.97	0.96	0.94	3	conclusive
GCA_016715965.1	s__UBA3362 sp016715965	79.0585	429	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA3362	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714365.1	s__UBA3362 sp016714365	78.8379	132	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA3362	95.0	99.03	97.76	0.92	0.86	12	-
GCA_016713905.1	s__UBA3362 sp016713905	77.6427	127	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA3362	95.0	99.28	99.28	0.96	0.96	2	-
GCA_016712225.1	s__UBA3362 sp016712225	76.9909	88	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA3362	95.0	96.22	95.32	0.83	0.80	5	-
GCA_016719615.1	s__UBA3362 sp016719615	76.5947	65	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA3362	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717265.1	s__UBA3362 sp016717265	76.4147	71	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__UBA3362	95.0	98.88	98.75	0.91	0.90	6	-
--------------------------------------------------------------------------------
[2023-06-29 22:59:14,573] [INFO] GTDB search result was written to GCA_016710265.1_ASM1671026v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:59:14,574] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:59:14,577] [INFO] DFAST_QC result json was written to GCA_016710265.1_ASM1671026v1_genomic.fna/dqc_result.json
[2023-06-29 22:59:14,578] [INFO] DFAST_QC completed!
[2023-06-29 22:59:14,578] [INFO] Total running time: 0h1m49s