[2023-06-28 17:40:03,634] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:40:03,638] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:40:03,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg843bf2af-8a3e-4408-b9df-4dc6545c721a/dqc_reference
[2023-06-28 17:40:04,879] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:40:04,880] [INFO] Task started: Prodigal
[2023-06-28 17:40:04,880] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf79248b-c031-48a6-98d7-f8a64f2c80d4/GCA_012964495.1_ASM1296449v1_genomic.fna.gz | prodigal -d GCA_012964495.1_ASM1296449v1_genomic.fna/cds.fna -a GCA_012964495.1_ASM1296449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:40:11,268] [INFO] Task succeeded: Prodigal
[2023-06-28 17:40:11,269] [INFO] Task started: HMMsearch
[2023-06-28 17:40:11,269] [INFO] Running command: hmmsearch --tblout GCA_012964495.1_ASM1296449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg843bf2af-8a3e-4408-b9df-4dc6545c721a/dqc_reference/reference_markers.hmm GCA_012964495.1_ASM1296449v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:40:11,513] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:40:11,515] [INFO] Found 6/6 markers.
[2023-06-28 17:40:11,542] [INFO] Query marker FASTA was written to GCA_012964495.1_ASM1296449v1_genomic.fna/markers.fasta
[2023-06-28 17:40:11,543] [INFO] Task started: Blastn
[2023-06-28 17:40:11,543] [INFO] Running command: blastn -query GCA_012964495.1_ASM1296449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg843bf2af-8a3e-4408-b9df-4dc6545c721a/dqc_reference/reference_markers.fasta -out GCA_012964495.1_ASM1296449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:40:12,117] [INFO] Task succeeded: Blastn
[2023-06-28 17:40:12,121] [INFO] Selected 12 target genomes.
[2023-06-28 17:40:12,122] [INFO] Target genome list was writen to GCA_012964495.1_ASM1296449v1_genomic.fna/target_genomes.txt
[2023-06-28 17:40:12,127] [INFO] Task started: fastANI
[2023-06-28 17:40:12,127] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf79248b-c031-48a6-98d7-f8a64f2c80d4/GCA_012964495.1_ASM1296449v1_genomic.fna.gz --refList GCA_012964495.1_ASM1296449v1_genomic.fna/target_genomes.txt --output GCA_012964495.1_ASM1296449v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:40:17,884] [INFO] Task succeeded: fastANI
[2023-06-28 17:40:17,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg843bf2af-8a3e-4408-b9df-4dc6545c721a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:40:17,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg843bf2af-8a3e-4408-b9df-4dc6545c721a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:40:17,887] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:40:17,887] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:40:17,888] [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 17:40:17,890] [INFO] DFAST Taxonomy check result was written to GCA_012964495.1_ASM1296449v1_genomic.fna/tc_result.tsv
[2023-06-28 17:40:17,891] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:40:17,891] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:40:17,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg843bf2af-8a3e-4408-b9df-4dc6545c721a/dqc_reference/checkm_data
[2023-06-28 17:40:17,895] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:40:17,931] [INFO] Task started: CheckM
[2023-06-28 17:40:17,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012964495.1_ASM1296449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012964495.1_ASM1296449v1_genomic.fna/checkm_input GCA_012964495.1_ASM1296449v1_genomic.fna/checkm_result
[2023-06-28 17:40:44,178] [INFO] Task succeeded: CheckM
[2023-06-28 17:40:44,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 7.12%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-28 17:40:44,209] [INFO] ===== Completeness check finished =====
[2023-06-28 17:40:44,210] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:40:44,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012964495.1_ASM1296449v1_genomic.fna/markers.fasta)
[2023-06-28 17:40:44,211] [INFO] Task started: Blastn
[2023-06-28 17:40:44,211] [INFO] Running command: blastn -query GCA_012964495.1_ASM1296449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg843bf2af-8a3e-4408-b9df-4dc6545c721a/dqc_reference/reference_markers_gtdb.fasta -out GCA_012964495.1_ASM1296449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:40:45,029] [INFO] Task succeeded: Blastn
[2023-06-28 17:40:45,034] [INFO] Selected 15 target genomes.
[2023-06-28 17:40:45,034] [INFO] Target genome list was writen to GCA_012964495.1_ASM1296449v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:40:45,074] [INFO] Task started: fastANI
[2023-06-28 17:40:45,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf79248b-c031-48a6-98d7-f8a64f2c80d4/GCA_012964495.1_ASM1296449v1_genomic.fna.gz --refList GCA_012964495.1_ASM1296449v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012964495.1_ASM1296449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:40:51,055] [INFO] Task succeeded: fastANI
[2023-06-28 17:40:51,066] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:40:51,066] [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_012964825.1	s__UBA2125 sp002311275	99.7124	655	746	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	99.57	99.39	0.92	0.84	10	conclusive
GCA_004124465.1	s__UBA2125 sp004124465	87.1318	345	746	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002329125.1	s__UBA2125 sp002329125	85.2333	416	746	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__UBA2125	95.0	97.65	95.42	0.79	0.68	5	-
GCA_002448795.1	s__S15-B10 sp002448795	76.6995	78	746	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__S15-B10	95.0	99.97	99.96	0.93	0.86	3	-
GCA_001626655.1	s__S15-B10 sp001626655	76.0825	52	746	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__S15-B10;g__S15-B10	95.0	98.13	97.75	0.76	0.70	4	-
--------------------------------------------------------------------------------
[2023-06-28 17:40:51,068] [INFO] GTDB search result was written to GCA_012964495.1_ASM1296449v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:40:51,069] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:40:51,071] [INFO] DFAST_QC result json was written to GCA_012964495.1_ASM1296449v1_genomic.fna/dqc_result.json
[2023-06-28 17:40:51,071] [INFO] DFAST_QC completed!
[2023-06-28 17:40:51,071] [INFO] Total running time: 0h0m47s