[2023-06-06 00:05:54,296] [INFO] DFAST_QC pipeline started.
[2023-06-06 00:05:54,298] [INFO] DFAST_QC version: 0.5.7
[2023-06-06 00:05:54,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d4bf24a-a2c2-40bd-8def-428ae8529a1f/dqc_reference
[2023-06-06 00:05:55,475] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-06 00:05:55,476] [INFO] Task started: Prodigal
[2023-06-06 00:05:55,476] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4abd831-698c-4a24-9930-261800d3d53d/GCA_010025265.1_ASM1002526v1_genomic.fna.gz | prodigal -d GCA_010025265.1_ASM1002526v1_genomic.fna/cds.fna -a GCA_010025265.1_ASM1002526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-06 00:06:07,730] [INFO] Task succeeded: Prodigal
[2023-06-06 00:06:07,730] [INFO] Task started: HMMsearch
[2023-06-06 00:06:07,731] [INFO] Running command: hmmsearch --tblout GCA_010025265.1_ASM1002526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d4bf24a-a2c2-40bd-8def-428ae8529a1f/dqc_reference/reference_markers.hmm GCA_010025265.1_ASM1002526v1_genomic.fna/protein.faa > /dev/null
[2023-06-06 00:06:07,906] [INFO] Task succeeded: HMMsearch
[2023-06-06 00:06:07,907] [INFO] Found 6/6 markers.
[2023-06-06 00:06:07,931] [INFO] Query marker FASTA was written to GCA_010025265.1_ASM1002526v1_genomic.fna/markers.fasta
[2023-06-06 00:06:07,931] [INFO] Task started: Blastn
[2023-06-06 00:06:07,931] [INFO] Running command: blastn -query GCA_010025265.1_ASM1002526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d4bf24a-a2c2-40bd-8def-428ae8529a1f/dqc_reference/reference_markers.fasta -out GCA_010025265.1_ASM1002526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:06:08,543] [INFO] Task succeeded: Blastn
[2023-06-06 00:06:08,547] [INFO] Selected 24 target genomes.
[2023-06-06 00:06:08,547] [INFO] Target genome list was writen to GCA_010025265.1_ASM1002526v1_genomic.fna/target_genomes.txt
[2023-06-06 00:06:08,552] [INFO] Task started: fastANI
[2023-06-06 00:06:08,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4abd831-698c-4a24-9930-261800d3d53d/GCA_010025265.1_ASM1002526v1_genomic.fna.gz --refList GCA_010025265.1_ASM1002526v1_genomic.fna/target_genomes.txt --output GCA_010025265.1_ASM1002526v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-06 00:06:23,360] [INFO] Task succeeded: fastANI
[2023-06-06 00:06:23,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d4bf24a-a2c2-40bd-8def-428ae8529a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-06 00:06:23,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d4bf24a-a2c2-40bd-8def-428ae8529a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-06 00:06:23,363] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-06 00:06:23,364] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-06 00:06:23,364] [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
--------------------------------------------------------------------------------
[2023-06-06 00:06:23,365] [INFO] DFAST Taxonomy check result was written to GCA_010025265.1_ASM1002526v1_genomic.fna/tc_result.tsv
[2023-06-06 00:06:23,366] [INFO] ===== Taxonomy check completed =====
[2023-06-06 00:06:23,366] [INFO] ===== Start completeness check using CheckM =====
[2023-06-06 00:06:23,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d4bf24a-a2c2-40bd-8def-428ae8529a1f/dqc_reference/checkm_data
[2023-06-06 00:06:23,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-06 00:06:23,389] [INFO] Task started: CheckM
[2023-06-06 00:06:23,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010025265.1_ASM1002526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010025265.1_ASM1002526v1_genomic.fna/checkm_input GCA_010025265.1_ASM1002526v1_genomic.fna/checkm_result
[2023-06-06 00:07:01,045] [INFO] Task succeeded: CheckM
[2023-06-06 00:07:01,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-06 00:07:01,063] [INFO] ===== Completeness check finished =====
[2023-06-06 00:07:01,063] [INFO] ===== Start GTDB Search =====
[2023-06-06 00:07:01,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010025265.1_ASM1002526v1_genomic.fna/markers.fasta)
[2023-06-06 00:07:01,063] [INFO] Task started: Blastn
[2023-06-06 00:07:01,064] [INFO] Running command: blastn -query GCA_010025265.1_ASM1002526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d4bf24a-a2c2-40bd-8def-428ae8529a1f/dqc_reference/reference_markers_gtdb.fasta -out GCA_010025265.1_ASM1002526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-06 00:07:02,391] [INFO] Task succeeded: Blastn
[2023-06-06 00:07:02,395] [INFO] Selected 19 target genomes.
[2023-06-06 00:07:02,395] [INFO] Target genome list was writen to GCA_010025265.1_ASM1002526v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-06 00:07:02,408] [INFO] Task started: fastANI
[2023-06-06 00:07:02,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4abd831-698c-4a24-9930-261800d3d53d/GCA_010025265.1_ASM1002526v1_genomic.fna.gz --refList GCA_010025265.1_ASM1002526v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010025265.1_ASM1002526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-06 00:07:11,623] [INFO] Task succeeded: fastANI
[2023-06-06 00:07:11,628] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-06 00:07:11,628] [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_002381225.1	s__TMED14 sp002381225	98.6446	495	583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	98.92	98.57	0.92	0.89	11	conclusive
GCA_003507115.1	s__TMED14 sp003507115	85.4062	315	583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	98.82	98.50	0.76	0.76	3	-
GCA_003444795.1	s__TMED14 sp003444795	79.2848	218	583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	99.24	99.24	0.85	0.85	2	-
GCA_001438205.1	s__TMED14 sp001438205	78.1806	158	583	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	99.81	99.57	0.95	0.91	8	-
--------------------------------------------------------------------------------
[2023-06-06 00:07:11,639] [INFO] GTDB search result was written to GCA_010025265.1_ASM1002526v1_genomic.fna/result_gtdb.tsv
[2023-06-06 00:07:11,640] [INFO] ===== GTDB Search completed =====
[2023-06-06 00:07:11,642] [INFO] DFAST_QC result json was written to GCA_010025265.1_ASM1002526v1_genomic.fna/dqc_result.json
[2023-06-06 00:07:11,642] [INFO] DFAST_QC completed!
[2023-06-06 00:07:11,642] [INFO] Total running time: 0h1m17s