[2023-06-27 05:39:06,806] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:39:06,834] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:39:06,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ce24517-fe8d-41da-851a-3e1fd7535443/dqc_reference
[2023-06-27 05:39:08,083] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:39:08,084] [INFO] Task started: Prodigal
[2023-06-27 05:39:08,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg48390182-027a-41bb-954d-fc620a408edd/GCA_002310075.1_ASM231007v1_genomic.fna.gz | prodigal -d GCA_002310075.1_ASM231007v1_genomic.fna/cds.fna -a GCA_002310075.1_ASM231007v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:39:22,281] [INFO] Task succeeded: Prodigal
[2023-06-27 05:39:22,281] [INFO] Task started: HMMsearch
[2023-06-27 05:39:22,281] [INFO] Running command: hmmsearch --tblout GCA_002310075.1_ASM231007v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ce24517-fe8d-41da-851a-3e1fd7535443/dqc_reference/reference_markers.hmm GCA_002310075.1_ASM231007v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:39:22,548] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:39:22,549] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg48390182-027a-41bb-954d-fc620a408edd/GCA_002310075.1_ASM231007v1_genomic.fna.gz]
[2023-06-27 05:39:22,580] [INFO] Query marker FASTA was written to GCA_002310075.1_ASM231007v1_genomic.fna/markers.fasta
[2023-06-27 05:39:22,580] [INFO] Task started: Blastn
[2023-06-27 05:39:22,581] [INFO] Running command: blastn -query GCA_002310075.1_ASM231007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ce24517-fe8d-41da-851a-3e1fd7535443/dqc_reference/reference_markers.fasta -out GCA_002310075.1_ASM231007v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:39:23,198] [INFO] Task succeeded: Blastn
[2023-06-27 05:39:23,202] [INFO] Selected 22 target genomes.
[2023-06-27 05:39:23,203] [INFO] Target genome list was writen to GCA_002310075.1_ASM231007v1_genomic.fna/target_genomes.txt
[2023-06-27 05:39:23,211] [INFO] Task started: fastANI
[2023-06-27 05:39:23,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg48390182-027a-41bb-954d-fc620a408edd/GCA_002310075.1_ASM231007v1_genomic.fna.gz --refList GCA_002310075.1_ASM231007v1_genomic.fna/target_genomes.txt --output GCA_002310075.1_ASM231007v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:39:40,027] [INFO] Task succeeded: fastANI
[2023-06-27 05:39:40,028] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ce24517-fe8d-41da-851a-3e1fd7535443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:39:40,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ce24517-fe8d-41da-851a-3e1fd7535443/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:39:40,046] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:39:40,046] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 05:39:40,046] [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 05:39:40,049] [INFO] DFAST Taxonomy check result was written to GCA_002310075.1_ASM231007v1_genomic.fna/tc_result.tsv
[2023-06-27 05:39:40,050] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:39:40,050] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:39:40,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ce24517-fe8d-41da-851a-3e1fd7535443/dqc_reference/checkm_data
[2023-06-27 05:39:40,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:39:40,082] [INFO] Task started: CheckM
[2023-06-27 05:39:40,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310075.1_ASM231007v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310075.1_ASM231007v1_genomic.fna/checkm_input GCA_002310075.1_ASM231007v1_genomic.fna/checkm_result
[2023-06-27 05:40:23,073] [INFO] Task succeeded: CheckM
[2023-06-27 05:40:23,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:40:23,096] [INFO] ===== Completeness check finished =====
[2023-06-27 05:40:23,097] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:40:23,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310075.1_ASM231007v1_genomic.fna/markers.fasta)
[2023-06-27 05:40:23,098] [INFO] Task started: Blastn
[2023-06-27 05:40:23,098] [INFO] Running command: blastn -query GCA_002310075.1_ASM231007v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ce24517-fe8d-41da-851a-3e1fd7535443/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310075.1_ASM231007v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:40:23,879] [INFO] Task succeeded: Blastn
[2023-06-27 05:40:23,898] [INFO] Selected 14 target genomes.
[2023-06-27 05:40:23,898] [INFO] Target genome list was writen to GCA_002310075.1_ASM231007v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:40:23,945] [INFO] Task started: fastANI
[2023-06-27 05:40:23,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg48390182-027a-41bb-954d-fc620a408edd/GCA_002310075.1_ASM231007v1_genomic.fna.gz --refList GCA_002310075.1_ASM231007v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310075.1_ASM231007v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:40:31,933] [INFO] Task succeeded: fastANI
[2023-06-27 05:40:31,947] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:40:31,947] [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_002310075.1	s__Limimorpha sp002310075	100.0	670	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.19	95.43	0.79	0.73	9	conclusive
GCA_902786745.1	s__Limimorpha sp902786745	83.8928	427	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.85	95.75	0.88	0.85	4	-
GCA_017539045.1	s__Limimorpha sp017539045	83.3385	373	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318265.1	s__Limimorpha sp900318265	81.6588	373	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.16	95.28	0.85	0.79	7	-
GCA_900318085.1	s__Limimorpha sp900318085	81.4863	396	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	97.28	96.84	0.87	0.80	12	-
GCA_017395365.1	s__Limimorpha sp017395365	81.0604	260	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774365.1	s__Limimorpha sp902774365	81.0414	371	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801625.1	s__Limimorpha sp902801625	80.9493	377	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799345.1	s__Limimorpha sp902799345	80.7743	374	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017632935.1	s__Limimorpha sp017632935	80.7095	348	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771635.1	s__Limimorpha sp902771635	80.4604	326	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651645.1	s__Limimorpha sp017651645	80.3343	341	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789915.1	s__Limimorpha sp902789915	80.1061	315	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.09	95.09	0.73	0.73	2	-
GCA_905233685.1	s__Limimorpha sp905233685	79.2488	304	675	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:40:31,949] [INFO] GTDB search result was written to GCA_002310075.1_ASM231007v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:40:31,950] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:40:31,953] [INFO] DFAST_QC result json was written to GCA_002310075.1_ASM231007v1_genomic.fna/dqc_result.json
[2023-06-27 05:40:31,953] [INFO] DFAST_QC completed!
[2023-06-27 05:40:31,953] [INFO] Total running time: 0h1m25s