[2023-06-05 04:14:19,291] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:14:19,293] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:14:19,294] [INFO] DQC Reference Directory: /var/lib/cwl/stg77c2da8e-ec22-471d-8367-b79594acab62/dqc_reference
[2023-06-05 04:14:20,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:14:20,719] [INFO] Task started: Prodigal
[2023-06-05 04:14:20,719] [INFO] Running command: gunzip -c /var/lib/cwl/stge8d2491a-8e75-4aca-bbf8-02e4fa3b6388/GCA_010024985.1_ASM1002498v1_genomic.fna.gz | prodigal -d GCA_010024985.1_ASM1002498v1_genomic.fna/cds.fna -a GCA_010024985.1_ASM1002498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:14:22,605] [INFO] Task succeeded: Prodigal
[2023-06-05 04:14:22,605] [INFO] Task started: HMMsearch
[2023-06-05 04:14:22,605] [INFO] Running command: hmmsearch --tblout GCA_010024985.1_ASM1002498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77c2da8e-ec22-471d-8367-b79594acab62/dqc_reference/reference_markers.hmm GCA_010024985.1_ASM1002498v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:14:22,830] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:14:22,832] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge8d2491a-8e75-4aca-bbf8-02e4fa3b6388/GCA_010024985.1_ASM1002498v1_genomic.fna.gz]
[2023-06-05 04:14:22,855] [INFO] Query marker FASTA was written to GCA_010024985.1_ASM1002498v1_genomic.fna/markers.fasta
[2023-06-05 04:14:22,856] [INFO] Task started: Blastn
[2023-06-05 04:14:22,856] [INFO] Running command: blastn -query GCA_010024985.1_ASM1002498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77c2da8e-ec22-471d-8367-b79594acab62/dqc_reference/reference_markers.fasta -out GCA_010024985.1_ASM1002498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:14:23,461] [INFO] Task succeeded: Blastn
[2023-06-05 04:14:23,465] [INFO] Selected 12 target genomes.
[2023-06-05 04:14:23,466] [INFO] Target genome list was writen to GCA_010024985.1_ASM1002498v1_genomic.fna/target_genomes.txt
[2023-06-05 04:14:23,492] [INFO] Task started: fastANI
[2023-06-05 04:14:23,492] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d2491a-8e75-4aca-bbf8-02e4fa3b6388/GCA_010024985.1_ASM1002498v1_genomic.fna.gz --refList GCA_010024985.1_ASM1002498v1_genomic.fna/target_genomes.txt --output GCA_010024985.1_ASM1002498v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:14:28,528] [INFO] Task succeeded: fastANI
[2023-06-05 04:14:28,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77c2da8e-ec22-471d-8367-b79594acab62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:14:28,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77c2da8e-ec22-471d-8367-b79594acab62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:14:28,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:14:28,530] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 04:14:28,531] [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
--------------------------------------------------------------------------------
[2023-06-05 04:14:28,533] [INFO] DFAST Taxonomy check result was written to GCA_010024985.1_ASM1002498v1_genomic.fna/tc_result.tsv
[2023-06-05 04:14:28,533] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:14:28,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:14:28,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77c2da8e-ec22-471d-8367-b79594acab62/dqc_reference/checkm_data
[2023-06-05 04:14:28,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:14:28,555] [INFO] Task started: CheckM
[2023-06-05 04:14:28,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010024985.1_ASM1002498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010024985.1_ASM1002498v1_genomic.fna/checkm_input GCA_010024985.1_ASM1002498v1_genomic.fna/checkm_result
[2023-06-05 04:14:43,031] [INFO] Task succeeded: CheckM
[2023-06-05 04:14:43,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:14:43,053] [INFO] ===== Completeness check finished =====
[2023-06-05 04:14:43,053] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:14:43,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010024985.1_ASM1002498v1_genomic.fna/markers.fasta)
[2023-06-05 04:14:43,054] [INFO] Task started: Blastn
[2023-06-05 04:14:43,054] [INFO] Running command: blastn -query GCA_010024985.1_ASM1002498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77c2da8e-ec22-471d-8367-b79594acab62/dqc_reference/reference_markers_gtdb.fasta -out GCA_010024985.1_ASM1002498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:14:43,837] [INFO] Task succeeded: Blastn
[2023-06-05 04:14:43,843] [INFO] Selected 6 target genomes.
[2023-06-05 04:14:43,843] [INFO] Target genome list was writen to GCA_010024985.1_ASM1002498v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:14:43,844] [INFO] Task started: fastANI
[2023-06-05 04:14:43,844] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d2491a-8e75-4aca-bbf8-02e4fa3b6388/GCA_010024985.1_ASM1002498v1_genomic.fna.gz --refList GCA_010024985.1_ASM1002498v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010024985.1_ASM1002498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:14:45,307] [INFO] Task succeeded: fastANI
[2023-06-05 04:14:45,318] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:14:45,318] [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_002347935.1	s__MAG-120802 sp002347935	99.0005	217	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	98.96	98.66	0.86	0.80	28	conclusive
GCA_003569145.1	s__MAG-120802 sp003569145	88.9317	211	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	99.02	99.02	0.96	0.96	2	-
GCA_016870795.1	s__MAG-120802 sp016870795	88.6116	202	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777515.1	s__MAG-120802 sp005777515	86.8294	158	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	98.53	98.39	0.77	0.76	3	-
GCA_016870365.1	s__MAG-120802 sp016870365	80.9289	177	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882745.1	s__MAG-120802 sp018882745	77.6481	77	258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:14:45,321] [INFO] GTDB search result was written to GCA_010024985.1_ASM1002498v1_genomic.fna/result_gtdb.tsv
[2023-06-05 04:14:45,322] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:14:45,325] [INFO] DFAST_QC result json was written to GCA_010024985.1_ASM1002498v1_genomic.fna/dqc_result.json
[2023-06-05 04:14:45,325] [INFO] DFAST_QC completed!
[2023-06-05 04:14:45,325] [INFO] Total running time: 0h0m26s