[2023-06-16 22:29:01,593] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:29:01,595] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:29:01,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdca8574-20a3-4abe-b820-2f15fe54e137/dqc_reference
[2023-06-16 22:29:03,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:29:03,587] [INFO] Task started: Prodigal
[2023-06-16 22:29:03,587] [INFO] Running command: gunzip -c /var/lib/cwl/stga45a49ef-b106-4721-93cd-09866134a356/GCA_009921005.1_ASM992100v1_genomic.fna.gz | prodigal -d GCA_009921005.1_ASM992100v1_genomic.fna/cds.fna -a GCA_009921005.1_ASM992100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:29:14,391] [INFO] Task succeeded: Prodigal
[2023-06-16 22:29:14,392] [INFO] Task started: HMMsearch
[2023-06-16 22:29:14,392] [INFO] Running command: hmmsearch --tblout GCA_009921005.1_ASM992100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdca8574-20a3-4abe-b820-2f15fe54e137/dqc_reference/reference_markers.hmm GCA_009921005.1_ASM992100v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:29:14,634] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:29:14,636] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga45a49ef-b106-4721-93cd-09866134a356/GCA_009921005.1_ASM992100v1_genomic.fna.gz]
[2023-06-16 22:29:14,662] [INFO] Query marker FASTA was written to GCA_009921005.1_ASM992100v1_genomic.fna/markers.fasta
[2023-06-16 22:29:14,662] [INFO] Task started: Blastn
[2023-06-16 22:29:14,662] [INFO] Running command: blastn -query GCA_009921005.1_ASM992100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdca8574-20a3-4abe-b820-2f15fe54e137/dqc_reference/reference_markers.fasta -out GCA_009921005.1_ASM992100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:29:15,230] [INFO] Task succeeded: Blastn
[2023-06-16 22:29:15,235] [INFO] Selected 21 target genomes.
[2023-06-16 22:29:15,236] [INFO] Target genome list was writen to GCA_009921005.1_ASM992100v1_genomic.fna/target_genomes.txt
[2023-06-16 22:29:15,241] [INFO] Task started: fastANI
[2023-06-16 22:29:15,241] [INFO] Running command: fastANI --query /var/lib/cwl/stga45a49ef-b106-4721-93cd-09866134a356/GCA_009921005.1_ASM992100v1_genomic.fna.gz --refList GCA_009921005.1_ASM992100v1_genomic.fna/target_genomes.txt --output GCA_009921005.1_ASM992100v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:29:31,259] [INFO] Task succeeded: fastANI
[2023-06-16 22:29:31,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdca8574-20a3-4abe-b820-2f15fe54e137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:29:31,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdca8574-20a3-4abe-b820-2f15fe54e137/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:29:31,262] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:29:31,263] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-16 22:29:31,263] [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 22:29:31,265] [INFO] DFAST Taxonomy check result was written to GCA_009921005.1_ASM992100v1_genomic.fna/tc_result.tsv
[2023-06-16 22:29:31,266] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:29:31,266] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:29:31,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdca8574-20a3-4abe-b820-2f15fe54e137/dqc_reference/checkm_data
[2023-06-16 22:29:31,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:29:31,300] [INFO] Task started: CheckM
[2023-06-16 22:29:31,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009921005.1_ASM992100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009921005.1_ASM992100v1_genomic.fna/checkm_input GCA_009921005.1_ASM992100v1_genomic.fna/checkm_result
[2023-06-16 22:30:06,371] [INFO] Task succeeded: CheckM
[2023-06-16 22:30:06,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-16 22:30:06,394] [INFO] ===== Completeness check finished =====
[2023-06-16 22:30:06,394] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:30:06,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009921005.1_ASM992100v1_genomic.fna/markers.fasta)
[2023-06-16 22:30:06,395] [INFO] Task started: Blastn
[2023-06-16 22:30:06,395] [INFO] Running command: blastn -query GCA_009921005.1_ASM992100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdca8574-20a3-4abe-b820-2f15fe54e137/dqc_reference/reference_markers_gtdb.fasta -out GCA_009921005.1_ASM992100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:30:07,130] [INFO] Task succeeded: Blastn
[2023-06-16 22:30:07,136] [INFO] Selected 21 target genomes.
[2023-06-16 22:30:07,136] [INFO] Target genome list was writen to GCA_009921005.1_ASM992100v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:30:07,155] [INFO] Task started: fastANI
[2023-06-16 22:30:07,155] [INFO] Running command: fastANI --query /var/lib/cwl/stga45a49ef-b106-4721-93cd-09866134a356/GCA_009921005.1_ASM992100v1_genomic.fna.gz --refList GCA_009921005.1_ASM992100v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009921005.1_ASM992100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:30:16,898] [INFO] Task succeeded: fastANI
[2023-06-16 22:30:16,907] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:30:16,907] [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_003489485.1	s__JJ008 sp003489485	96.0877	354	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.38	96.92	0.79	0.76	3	conclusive
GCA_016872155.1	s__JJ008 sp016872155	79.7326	336	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872195.1	s__JJ008 sp016872195	78.6296	276	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342205.1	s__JJ008 sp002342205	76.7178	69	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.68	98.09	0.85	0.80	4	-
GCA_016868475.1	s__JJ008 sp016868475	76.2746	55	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789565.1	s__JJ008 sp005789565	76.1711	50	576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:30:16,909] [INFO] GTDB search result was written to GCA_009921005.1_ASM992100v1_genomic.fna/result_gtdb.tsv
[2023-06-16 22:30:16,910] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:30:16,912] [INFO] DFAST_QC result json was written to GCA_009921005.1_ASM992100v1_genomic.fna/dqc_result.json
[2023-06-16 22:30:16,912] [INFO] DFAST_QC completed!
[2023-06-16 22:30:16,913] [INFO] Total running time: 0h1m15s