[2023-06-28 04:59:16,892] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:59:16,894] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:59:16,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg17872d5c-8fc2-4338-b4a7-a83fada83bf1/dqc_reference
[2023-06-28 04:59:18,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:59:18,101] [INFO] Task started: Prodigal
[2023-06-28 04:59:18,102] [INFO] Running command: gunzip -c /var/lib/cwl/stg453fa01d-d4dd-467b-a50f-01806a6ef620/GCA_017385585.1_ASM1738558v1_genomic.fna.gz | prodigal -d GCA_017385585.1_ASM1738558v1_genomic.fna/cds.fna -a GCA_017385585.1_ASM1738558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:59:23,412] [INFO] Task succeeded: Prodigal
[2023-06-28 04:59:23,412] [INFO] Task started: HMMsearch
[2023-06-28 04:59:23,413] [INFO] Running command: hmmsearch --tblout GCA_017385585.1_ASM1738558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17872d5c-8fc2-4338-b4a7-a83fada83bf1/dqc_reference/reference_markers.hmm GCA_017385585.1_ASM1738558v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:59:23,613] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:59:23,615] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg453fa01d-d4dd-467b-a50f-01806a6ef620/GCA_017385585.1_ASM1738558v1_genomic.fna.gz]
[2023-06-28 04:59:23,643] [INFO] Query marker FASTA was written to GCA_017385585.1_ASM1738558v1_genomic.fna/markers.fasta
[2023-06-28 04:59:23,644] [INFO] Task started: Blastn
[2023-06-28 04:59:23,644] [INFO] Running command: blastn -query GCA_017385585.1_ASM1738558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17872d5c-8fc2-4338-b4a7-a83fada83bf1/dqc_reference/reference_markers.fasta -out GCA_017385585.1_ASM1738558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:24,203] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:24,206] [INFO] Selected 10 target genomes.
[2023-06-28 04:59:24,206] [INFO] Target genome list was writen to GCA_017385585.1_ASM1738558v1_genomic.fna/target_genomes.txt
[2023-06-28 04:59:24,208] [INFO] Task started: fastANI
[2023-06-28 04:59:24,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg453fa01d-d4dd-467b-a50f-01806a6ef620/GCA_017385585.1_ASM1738558v1_genomic.fna.gz --refList GCA_017385585.1_ASM1738558v1_genomic.fna/target_genomes.txt --output GCA_017385585.1_ASM1738558v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:59:28,213] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:28,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17872d5c-8fc2-4338-b4a7-a83fada83bf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:59:28,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17872d5c-8fc2-4338-b4a7-a83fada83bf1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:59:28,215] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:59:28,215] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:59:28,215] [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
--------------------------------------------------------------------------------
[2023-06-28 04:59:28,217] [INFO] DFAST Taxonomy check result was written to GCA_017385585.1_ASM1738558v1_genomic.fna/tc_result.tsv
[2023-06-28 04:59:28,218] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:59:28,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:59:28,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17872d5c-8fc2-4338-b4a7-a83fada83bf1/dqc_reference/checkm_data
[2023-06-28 04:59:28,221] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:59:28,248] [INFO] Task started: CheckM
[2023-06-28 04:59:28,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017385585.1_ASM1738558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017385585.1_ASM1738558v1_genomic.fna/checkm_input GCA_017385585.1_ASM1738558v1_genomic.fna/checkm_result
[2023-06-28 04:59:50,449] [INFO] Task succeeded: CheckM
[2023-06-28 04:59:50,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 10.42%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-28 04:59:50,469] [INFO] ===== Completeness check finished =====
[2023-06-28 04:59:50,470] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:59:50,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017385585.1_ASM1738558v1_genomic.fna/markers.fasta)
[2023-06-28 04:59:50,470] [INFO] Task started: Blastn
[2023-06-28 04:59:50,470] [INFO] Running command: blastn -query GCA_017385585.1_ASM1738558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17872d5c-8fc2-4338-b4a7-a83fada83bf1/dqc_reference/reference_markers_gtdb.fasta -out GCA_017385585.1_ASM1738558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:59:51,264] [INFO] Task succeeded: Blastn
[2023-06-28 04:59:51,268] [INFO] Selected 11 target genomes.
[2023-06-28 04:59:51,269] [INFO] Target genome list was writen to GCA_017385585.1_ASM1738558v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:59:51,307] [INFO] Task started: fastANI
[2023-06-28 04:59:51,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg453fa01d-d4dd-467b-a50f-01806a6ef620/GCA_017385585.1_ASM1738558v1_genomic.fna.gz --refList GCA_017385585.1_ASM1738558v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017385585.1_ASM1738558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:59:57,676] [INFO] Task succeeded: fastANI
[2023-06-28 04:59:57,682] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 04:59:57,682] [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_017652685.1	s__Limivicinus sp017652685	85.3679	197	488	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_017406005.1	s__Limivicinus sp017406005	83.6932	204	488	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_017469115.1	s__Limivicinus sp017469115	80.3393	133	488	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_902778665.1	s__Limivicinus sp902778665	79.6506	112	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.10	97.03	0.78	0.73	4	-
GCA_017448455.1	s__Limivicinus sp017448455	78.277	51	488	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_017432615.1	s__Limivicinus sp017432615	78.2497	57	488	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.51	98.51	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-28 04:59:57,694] [INFO] GTDB search result was written to GCA_017385585.1_ASM1738558v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:59:57,695] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:59:57,697] [INFO] DFAST_QC result json was written to GCA_017385585.1_ASM1738558v1_genomic.fna/dqc_result.json
[2023-06-28 04:59:57,697] [INFO] DFAST_QC completed!
[2023-06-28 04:59:57,697] [INFO] Total running time: 0h0m41s