[2023-06-27 16:55:45,588] [INFO] DFAST_QC pipeline started.
[2023-06-27 16:55:45,590] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 16:55:45,590] [INFO] DQC Reference Directory: /var/lib/cwl/stge279a737-05ec-4f5d-ac0f-f9477959dcc7/dqc_reference
[2023-06-27 16:55:46,903] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 16:55:46,904] [INFO] Task started: Prodigal
[2023-06-27 16:55:46,905] [INFO] Running command: gunzip -c /var/lib/cwl/stg345174c6-50a8-4fd0-a52b-50b29821edbe/GCA_002449835.1_ASM244983v1_genomic.fna.gz | prodigal -d GCA_002449835.1_ASM244983v1_genomic.fna/cds.fna -a GCA_002449835.1_ASM244983v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 16:55:50,492] [INFO] Task succeeded: Prodigal
[2023-06-27 16:55:50,492] [INFO] Task started: HMMsearch
[2023-06-27 16:55:50,492] [INFO] Running command: hmmsearch --tblout GCA_002449835.1_ASM244983v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge279a737-05ec-4f5d-ac0f-f9477959dcc7/dqc_reference/reference_markers.hmm GCA_002449835.1_ASM244983v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 16:55:50,704] [INFO] Task succeeded: HMMsearch
[2023-06-27 16:55:50,706] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg345174c6-50a8-4fd0-a52b-50b29821edbe/GCA_002449835.1_ASM244983v1_genomic.fna.gz]
[2023-06-27 16:55:50,732] [INFO] Query marker FASTA was written to GCA_002449835.1_ASM244983v1_genomic.fna/markers.fasta
[2023-06-27 16:55:50,732] [INFO] Task started: Blastn
[2023-06-27 16:55:50,732] [INFO] Running command: blastn -query GCA_002449835.1_ASM244983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge279a737-05ec-4f5d-ac0f-f9477959dcc7/dqc_reference/reference_markers.fasta -out GCA_002449835.1_ASM244983v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 16:55:51,339] [INFO] Task succeeded: Blastn
[2023-06-27 16:55:51,342] [INFO] Selected 14 target genomes.
[2023-06-27 16:55:51,343] [INFO] Target genome list was writen to GCA_002449835.1_ASM244983v1_genomic.fna/target_genomes.txt
[2023-06-27 16:55:51,348] [INFO] Task started: fastANI
[2023-06-27 16:55:51,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg345174c6-50a8-4fd0-a52b-50b29821edbe/GCA_002449835.1_ASM244983v1_genomic.fna.gz --refList GCA_002449835.1_ASM244983v1_genomic.fna/target_genomes.txt --output GCA_002449835.1_ASM244983v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 16:55:58,351] [INFO] Task succeeded: fastANI
[2023-06-27 16:55:58,352] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge279a737-05ec-4f5d-ac0f-f9477959dcc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 16:55:58,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge279a737-05ec-4f5d-ac0f-f9477959dcc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 16:55:58,354] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 16:55:58,354] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 16:55:58,354] [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
--------------------------------------------------------------------------------
[2023-06-27 16:55:58,356] [INFO] DFAST Taxonomy check result was written to GCA_002449835.1_ASM244983v1_genomic.fna/tc_result.tsv
[2023-06-27 16:55:58,357] [INFO] ===== Taxonomy check completed =====
[2023-06-27 16:55:58,357] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 16:55:58,358] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge279a737-05ec-4f5d-ac0f-f9477959dcc7/dqc_reference/checkm_data
[2023-06-27 16:55:58,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 16:55:58,383] [INFO] Task started: CheckM
[2023-06-27 16:55:58,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002449835.1_ASM244983v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002449835.1_ASM244983v1_genomic.fna/checkm_input GCA_002449835.1_ASM244983v1_genomic.fna/checkm_result
[2023-06-27 16:56:15,796] [INFO] Task succeeded: CheckM
[2023-06-27 16:56:15,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 16:56:15,817] [INFO] ===== Completeness check finished =====
[2023-06-27 16:56:15,818] [INFO] ===== Start GTDB Search =====
[2023-06-27 16:56:15,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002449835.1_ASM244983v1_genomic.fna/markers.fasta)
[2023-06-27 16:56:15,818] [INFO] Task started: Blastn
[2023-06-27 16:56:15,818] [INFO] Running command: blastn -query GCA_002449835.1_ASM244983v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge279a737-05ec-4f5d-ac0f-f9477959dcc7/dqc_reference/reference_markers_gtdb.fasta -out GCA_002449835.1_ASM244983v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 16:56:16,814] [INFO] Task succeeded: Blastn
[2023-06-27 16:56:16,818] [INFO] Selected 10 target genomes.
[2023-06-27 16:56:16,818] [INFO] Target genome list was writen to GCA_002449835.1_ASM244983v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 16:56:16,845] [INFO] Task started: fastANI
[2023-06-27 16:56:16,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg345174c6-50a8-4fd0-a52b-50b29821edbe/GCA_002449835.1_ASM244983v1_genomic.fna.gz --refList GCA_002449835.1_ASM244983v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002449835.1_ASM244983v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 16:56:20,976] [INFO] Task succeeded: fastANI
[2023-06-27 16:56:20,991] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 16:56:20,991] [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_002450075.1	s__Limivicinus sp002450075	98.0376	360	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.03	97.77	0.79	0.75	6	conclusive
GCA_900320595.1	s__Limivicinus sp900320595	93.9403	362	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.20	98.25	0.89	0.82	4	-
GCA_017444665.1	s__Limivicinus sp017444665	88.5716	261	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319935.1	s__Limivicinus sp900319935	84.2762	265	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.02	98.62	0.86	0.80	6	-
GCA_902761055.1	s__Limivicinus sp902761055	84.1405	273	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320465.1	s__Limivicinus sp900320465	83.9952	292	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017447645.1	s__Limivicinus sp017447645	83.6603	247	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017403885.1	s__Limivicinus sp017403885	83.261	274	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778115.1	s__Limivicinus sp902778115	81.0965	235	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.60	97.29	0.87	0.83	3	-
GCA_900319835.1	s__Limivicinus sp900319835	80.7277	184	444	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-27 16:56:20,994] [INFO] GTDB search result was written to GCA_002449835.1_ASM244983v1_genomic.fna/result_gtdb.tsv
[2023-06-27 16:56:20,995] [INFO] ===== GTDB Search completed =====
[2023-06-27 16:56:20,998] [INFO] DFAST_QC result json was written to GCA_002449835.1_ASM244983v1_genomic.fna/dqc_result.json
[2023-06-27 16:56:20,998] [INFO] DFAST_QC completed!
[2023-06-27 16:56:20,998] [INFO] Total running time: 0h0m35s