[2024-01-24 13:18:41,534] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg153a29ef-23a4-40ad-b549-cd314d56657b/dqc_reference
[2024-01-24 13:18:42,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,738] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f6526c2-6a8c-40e0-aa2b-13cb37dca1c0/GCF_013415235.1_ASM1341523v1_genomic.fna.gz | prodigal -d GCF_013415235.1_ASM1341523v1_genomic.fna/cds.fna -a GCF_013415235.1_ASM1341523v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:45,264] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:45,264] [INFO] Task started: HMMsearch
[2024-01-24 13:18:45,265] [INFO] Running command: hmmsearch --tblout GCF_013415235.1_ASM1341523v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg153a29ef-23a4-40ad-b549-cd314d56657b/dqc_reference/reference_markers.hmm GCF_013415235.1_ASM1341523v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:45,475] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:45,477] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7f6526c2-6a8c-40e0-aa2b-13cb37dca1c0/GCF_013415235.1_ASM1341523v1_genomic.fna.gz]
[2024-01-24 13:18:45,504] [INFO] Query marker FASTA was written to GCF_013415235.1_ASM1341523v1_genomic.fna/markers.fasta
[2024-01-24 13:18:45,504] [INFO] Task started: Blastn
[2024-01-24 13:18:45,504] [INFO] Running command: blastn -query GCF_013415235.1_ASM1341523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153a29ef-23a4-40ad-b549-cd314d56657b/dqc_reference/reference_markers.fasta -out GCF_013415235.1_ASM1341523v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:46,082] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:46,085] [INFO] Selected 26 target genomes.
[2024-01-24 13:18:46,085] [INFO] Target genome list was writen to GCF_013415235.1_ASM1341523v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:46,127] [INFO] Task started: fastANI
[2024-01-24 13:18:46,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f6526c2-6a8c-40e0-aa2b-13cb37dca1c0/GCF_013415235.1_ASM1341523v1_genomic.fna.gz --refList GCF_013415235.1_ASM1341523v1_genomic.fna/target_genomes.txt --output GCF_013415235.1_ASM1341523v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:55,503] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,504] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg153a29ef-23a4-40ad-b549-cd314d56657b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:55,504] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg153a29ef-23a4-40ad-b549-cd314d56657b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:55,515] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:55,515] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:55,515] [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
Gemella sanguinis	strain=ATCC 700632	GCA_000701685.1	84135	84135	type	True	78.2465	145	554	95	below_threshold
Gemella haemolysans	strain=CCUG 37985T	GCA_008692995.1	1379	1379	suspected-type	True	78.1276	117	554	95	below_threshold
Gemella haemolysans	strain=ATCC 10379	GCA_000173915.1	1379	1379	suspected-type	True	78.0612	120	554	95	below_threshold
Gemella massiliensis	strain=Marseille-P3249	GCA_900120125.1	1909670	1909670	type	True	77.7153	109	554	95	below_threshold
Gemella bergeri	strain=ATCC 700627	GCA_000469465.1	84136	84136	type	True	77.5459	100	554	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	74.7579	51	554	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	74.744	52	554	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	74.7263	60	554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,517] [INFO] DFAST Taxonomy check result was written to GCF_013415235.1_ASM1341523v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:55,517] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:55,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:55,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg153a29ef-23a4-40ad-b549-cd314d56657b/dqc_reference/checkm_data
[2024-01-24 13:18:55,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:55,587] [INFO] Task started: CheckM
[2024-01-24 13:18:55,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013415235.1_ASM1341523v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013415235.1_ASM1341523v1_genomic.fna/checkm_input GCF_013415235.1_ASM1341523v1_genomic.fna/checkm_result
[2024-01-24 13:19:11,621] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:11,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:11,640] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:11,641] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:11,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013415235.1_ASM1341523v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:11,642] [INFO] Task started: Blastn
[2024-01-24 13:19:11,642] [INFO] Running command: blastn -query GCF_013415235.1_ASM1341523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg153a29ef-23a4-40ad-b549-cd314d56657b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013415235.1_ASM1341523v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:12,421] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:12,426] [INFO] Selected 20 target genomes.
[2024-01-24 13:19:12,426] [INFO] Target genome list was writen to GCF_013415235.1_ASM1341523v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:12,484] [INFO] Task started: fastANI
[2024-01-24 13:19:12,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f6526c2-6a8c-40e0-aa2b-13cb37dca1c0/GCF_013415235.1_ASM1341523v1_genomic.fna.gz --refList GCF_013415235.1_ASM1341523v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013415235.1_ASM1341523v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:19,429] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:19,438] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:19,438] [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
GCF_013415235.1	s__Gemella palaticanis	100.0	553	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013415365.1	s__Gemella sp004570485	79.1311	96	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.83	99.74	0.98	0.97	4	-
GCF_018866345.1	s__Gemella sp018866345	79.1015	177	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.31	99.31	0.99	0.99	2	-
GCF_013415425.1	s__Gemella sp013415425	78.9652	202	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012273215.1	s__Gemella haemolysans_A	78.4941	127	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	99.95	99.95	0.99	0.99	2	-
GCA_002871655.1	s__Gemella sp002871655	78.2667	141	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	98.42	98.42	0.93	0.93	2	-
GCF_000701685.1	s__Gemella sanguinis	78.2228	146	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	97.27	96.22	0.93	0.90	6	-
GCA_900766305.1	s__Gemella sp900766305	77.9503	116	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553005.1	s__Gemella asaccharolytica	77.5879	148	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000469465.1	s__Gemella bergeri	77.5459	100	554	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:19,440] [INFO] GTDB search result was written to GCF_013415235.1_ASM1341523v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:19,441] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:19,501] [INFO] DFAST_QC result json was written to GCF_013415235.1_ASM1341523v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:19,501] [INFO] DFAST_QC completed!
[2024-01-24 13:19:19,501] [INFO] Total running time: 0h0m38s