[2023-06-08 12:31:47,543] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:31:47,549] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:31:47,549] [INFO] DQC Reference Directory: /var/lib/cwl/stga84aad85-bb93-4144-b66c-f1578fd00842/dqc_reference
[2023-06-08 12:31:48,793] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:31:48,793] [INFO] Task started: Prodigal
[2023-06-08 12:31:48,794] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e49ef13-c278-47f6-b7b3-129fd5e8a0d3/GCA_947504685.1_ZH-Jul18-100_genomic.fna.gz | prodigal -d GCA_947504685.1_ZH-Jul18-100_genomic.fna/cds.fna -a GCA_947504685.1_ZH-Jul18-100_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:31:52,218] [INFO] Task succeeded: Prodigal
[2023-06-08 12:31:52,219] [INFO] Task started: HMMsearch
[2023-06-08 12:31:52,219] [INFO] Running command: hmmsearch --tblout GCA_947504685.1_ZH-Jul18-100_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga84aad85-bb93-4144-b66c-f1578fd00842/dqc_reference/reference_markers.hmm GCA_947504685.1_ZH-Jul18-100_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:31:52,428] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:31:52,430] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6e49ef13-c278-47f6-b7b3-129fd5e8a0d3/GCA_947504685.1_ZH-Jul18-100_genomic.fna.gz]
[2023-06-08 12:31:52,449] [INFO] Query marker FASTA was written to GCA_947504685.1_ZH-Jul18-100_genomic.fna/markers.fasta
[2023-06-08 12:31:52,449] [INFO] Task started: Blastn
[2023-06-08 12:31:52,449] [INFO] Running command: blastn -query GCA_947504685.1_ZH-Jul18-100_genomic.fna/markers.fasta -db /var/lib/cwl/stga84aad85-bb93-4144-b66c-f1578fd00842/dqc_reference/reference_markers.fasta -out GCA_947504685.1_ZH-Jul18-100_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:31:53,037] [INFO] Task succeeded: Blastn
[2023-06-08 12:31:53,042] [INFO] Selected 22 target genomes.
[2023-06-08 12:31:53,043] [INFO] Target genome list was writen to GCA_947504685.1_ZH-Jul18-100_genomic.fna/target_genomes.txt
[2023-06-08 12:31:53,045] [INFO] Task started: fastANI
[2023-06-08 12:31:53,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e49ef13-c278-47f6-b7b3-129fd5e8a0d3/GCA_947504685.1_ZH-Jul18-100_genomic.fna.gz --refList GCA_947504685.1_ZH-Jul18-100_genomic.fna/target_genomes.txt --output GCA_947504685.1_ZH-Jul18-100_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:32:06,860] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:06,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga84aad85-bb93-4144-b66c-f1578fd00842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:32:06,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga84aad85-bb93-4144-b66c-f1578fd00842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:32:06,864] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:32:06,864] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:32:06,864] [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
--------------------------------------------------------------------------------
[2023-06-08 12:32:06,866] [INFO] DFAST Taxonomy check result was written to GCA_947504685.1_ZH-Jul18-100_genomic.fna/tc_result.tsv
[2023-06-08 12:32:06,867] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:32:06,867] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:32:06,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga84aad85-bb93-4144-b66c-f1578fd00842/dqc_reference/checkm_data
[2023-06-08 12:32:06,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:32:06,890] [INFO] Task started: CheckM
[2023-06-08 12:32:06,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947504685.1_ZH-Jul18-100_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947504685.1_ZH-Jul18-100_genomic.fna/checkm_input GCA_947504685.1_ZH-Jul18-100_genomic.fna/checkm_result
[2023-06-08 12:32:23,803] [INFO] Task succeeded: CheckM
[2023-06-08 12:32:23,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 35.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:32:23,833] [INFO] ===== Completeness check finished =====
[2023-06-08 12:32:23,833] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:32:23,834] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947504685.1_ZH-Jul18-100_genomic.fna/markers.fasta)
[2023-06-08 12:32:23,834] [INFO] Task started: Blastn
[2023-06-08 12:32:23,834] [INFO] Running command: blastn -query GCA_947504685.1_ZH-Jul18-100_genomic.fna/markers.fasta -db /var/lib/cwl/stga84aad85-bb93-4144-b66c-f1578fd00842/dqc_reference/reference_markers_gtdb.fasta -out GCA_947504685.1_ZH-Jul18-100_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:32:24,674] [INFO] Task succeeded: Blastn
[2023-06-08 12:32:24,678] [INFO] Selected 8 target genomes.
[2023-06-08 12:32:24,678] [INFO] Target genome list was writen to GCA_947504685.1_ZH-Jul18-100_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:32:24,679] [INFO] Task started: fastANI
[2023-06-08 12:32:24,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e49ef13-c278-47f6-b7b3-129fd5e8a0d3/GCA_947504685.1_ZH-Jul18-100_genomic.fna.gz --refList GCA_947504685.1_ZH-Jul18-100_genomic.fna/target_genomes_gtdb.txt --output GCA_947504685.1_ZH-Jul18-100_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:32:27,237] [INFO] Task succeeded: fastANI
[2023-06-08 12:32:27,249] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:32:27,249] [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_009693615.1	s__Sediminibacterium sp009693615	97.4271	216	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013205585.1	s__Sediminibacterium sp013205585	92.8695	214	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280515.1	s__Sediminibacterium sp007280515	90.0599	243	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903825095.1	s__Sediminibacterium sp903825095	87.5444	195	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.41	98.41	0.71	0.71	2	-
GCA_009928005.1	s__Sediminibacterium sp009928005	87.0451	245	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.65	99.49	0.90	0.88	3	-
GCA_903854725.1	s__Sediminibacterium sp903854725	83.1614	239	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.67	99.52	0.89	0.86	5	-
GCA_903865435.1	s__Sediminibacterium sp903865435	81.7435	217	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.68	99.46	0.94	0.90	16	-
GCA_903847655.1	s__Sediminibacterium sp903847655	81.0223	168	281	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:32:27,251] [INFO] GTDB search result was written to GCA_947504685.1_ZH-Jul18-100_genomic.fna/result_gtdb.tsv
[2023-06-08 12:32:27,252] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:32:27,254] [INFO] DFAST_QC result json was written to GCA_947504685.1_ZH-Jul18-100_genomic.fna/dqc_result.json
[2023-06-08 12:32:27,254] [INFO] DFAST_QC completed!
[2023-06-08 12:32:27,254] [INFO] Total running time: 0h0m40s