[2024-01-25 20:12:20,875] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:20,876] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:20,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg82c1acae-2022-4285-9e45-cfdce12c5872/dqc_reference
[2024-01-25 20:12:22,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:22,152] [INFO] Task started: Prodigal
[2024-01-25 20:12:22,153] [INFO] Running command: gunzip -c /var/lib/cwl/stg693decfe-596c-439a-917d-05f428102018/GCF_024341905.1_ASM2434190v1_genomic.fna.gz | prodigal -d GCF_024341905.1_ASM2434190v1_genomic.fna/cds.fna -a GCF_024341905.1_ASM2434190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:29,720] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:29,720] [INFO] Task started: HMMsearch
[2024-01-25 20:12:29,720] [INFO] Running command: hmmsearch --tblout GCF_024341905.1_ASM2434190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82c1acae-2022-4285-9e45-cfdce12c5872/dqc_reference/reference_markers.hmm GCF_024341905.1_ASM2434190v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:29,986] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:29,988] [INFO] Found 6/6 markers.
[2024-01-25 20:12:30,025] [INFO] Query marker FASTA was written to GCF_024341905.1_ASM2434190v1_genomic.fna/markers.fasta
[2024-01-25 20:12:30,025] [INFO] Task started: Blastn
[2024-01-25 20:12:30,025] [INFO] Running command: blastn -query GCF_024341905.1_ASM2434190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82c1acae-2022-4285-9e45-cfdce12c5872/dqc_reference/reference_markers.fasta -out GCF_024341905.1_ASM2434190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:30,582] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:30,585] [INFO] Selected 21 target genomes.
[2024-01-25 20:12:30,585] [INFO] Target genome list was writen to GCF_024341905.1_ASM2434190v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:30,599] [INFO] Task started: fastANI
[2024-01-25 20:12:30,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg693decfe-596c-439a-917d-05f428102018/GCF_024341905.1_ASM2434190v1_genomic.fna.gz --refList GCF_024341905.1_ASM2434190v1_genomic.fna/target_genomes.txt --output GCF_024341905.1_ASM2434190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:51,053] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:51,054] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82c1acae-2022-4285-9e45-cfdce12c5872/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:51,054] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82c1acae-2022-4285-9e45-cfdce12c5872/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:51,068] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:12:51,068] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:12:51,068] [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
Clostridium fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	91.2402	1515	1768	95	below_threshold
Clostridium zeae	strain=CSC2	GCA_017312485.1	2759022	2759022	type	True	90.118	1482	1768	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	81.0212	856	1768	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	77.3929	243	1768	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	77.1314	222	1768	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	77.1116	223	1768	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.0383	176	1768	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	76.9512	191	1768	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	76.923	211	1768	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.9191	225	1768	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008580445.1	223919	223919	suspected-type	True	76.907	226	1768	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	76.8965	174	1768	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	76.686	172	1768	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	76.6783	174	1768	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.6703	188	1768	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.6582	140	1768	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.631	201	1768	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.5967	173	1768	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	76.5227	181	1768	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	76.5099	149	1768	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	75.8665	120	1768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:51,071] [INFO] DFAST Taxonomy check result was written to GCF_024341905.1_ASM2434190v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:51,072] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:51,073] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:51,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82c1acae-2022-4285-9e45-cfdce12c5872/dqc_reference/checkm_data
[2024-01-25 20:12:51,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:51,127] [INFO] Task started: CheckM
[2024-01-25 20:12:51,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024341905.1_ASM2434190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024341905.1_ASM2434190v1_genomic.fna/checkm_input GCF_024341905.1_ASM2434190v1_genomic.fna/checkm_result
[2024-01-25 20:13:17,766] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:17,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:17,789] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:17,790] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:17,790] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024341905.1_ASM2434190v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:17,790] [INFO] Task started: Blastn
[2024-01-25 20:13:17,790] [INFO] Running command: blastn -query GCF_024341905.1_ASM2434190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82c1acae-2022-4285-9e45-cfdce12c5872/dqc_reference/reference_markers_gtdb.fasta -out GCF_024341905.1_ASM2434190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:18,574] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:18,578] [INFO] Selected 8 target genomes.
[2024-01-25 20:13:18,578] [INFO] Target genome list was writen to GCF_024341905.1_ASM2434190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:18,596] [INFO] Task started: fastANI
[2024-01-25 20:13:18,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg693decfe-596c-439a-917d-05f428102018/GCF_024341905.1_ASM2434190v1_genomic.fna.gz --refList GCF_024341905.1_ASM2434190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024341905.1_ASM2434190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:13:29,885] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:29,891] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:13:29,892] [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_014193895.1	s__Clostridium_AR fungisolvens	91.2386	1515	1768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017312485.1	s__Clostridium_AR sp017312485	90.1104	1483	1768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595795.1	s__Clostridium_AR sp016595795	89.5066	1361	1768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004015185.1	s__Clostridium_AR sp004015185	80.9862	862	1768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928445.1	s__Clostridium_AR sp009928445	80.9692	843	1768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003606265.1	s__Clostridium septicum	77.1997	161	1768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_001458595.1	s__Clostridium neonatale	76.6937	173	1768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.07	98.42	0.91	0.80	11	-
GCA_018372555.1	s__Clostridium sp018372555	76.3727	143	1768	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:13:29,896] [INFO] GTDB search result was written to GCF_024341905.1_ASM2434190v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:13:29,897] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:13:29,900] [INFO] DFAST_QC result json was written to GCF_024341905.1_ASM2434190v1_genomic.fna/dqc_result.json
[2024-01-25 20:13:29,901] [INFO] DFAST_QC completed!
[2024-01-25 20:13:29,901] [INFO] Total running time: 0h1m9s