[2024-01-25 19:57:50,693] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:50,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:50,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c225733-54a6-473e-a1c6-cb98fab256e9/dqc_reference
[2024-01-25 19:57:51,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:51,896] [INFO] Task started: Prodigal
[2024-01-25 19:57:51,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg76e33103-2e41-4ea0-a1eb-f1e9de79562c/GCF_025370255.1_ASM2537025v1_genomic.fna.gz | prodigal -d GCF_025370255.1_ASM2537025v1_genomic.fna/cds.fna -a GCF_025370255.1_ASM2537025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:59,938] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:59,938] [INFO] Task started: HMMsearch
[2024-01-25 19:57:59,938] [INFO] Running command: hmmsearch --tblout GCF_025370255.1_ASM2537025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c225733-54a6-473e-a1c6-cb98fab256e9/dqc_reference/reference_markers.hmm GCF_025370255.1_ASM2537025v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:00,207] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:00,208] [INFO] Found 6/6 markers.
[2024-01-25 19:58:00,243] [INFO] Query marker FASTA was written to GCF_025370255.1_ASM2537025v1_genomic.fna/markers.fasta
[2024-01-25 19:58:00,243] [INFO] Task started: Blastn
[2024-01-25 19:58:00,243] [INFO] Running command: blastn -query GCF_025370255.1_ASM2537025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c225733-54a6-473e-a1c6-cb98fab256e9/dqc_reference/reference_markers.fasta -out GCF_025370255.1_ASM2537025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:00,940] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:00,946] [INFO] Selected 14 target genomes.
[2024-01-25 19:58:00,947] [INFO] Target genome list was writen to GCF_025370255.1_ASM2537025v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:00,963] [INFO] Task started: fastANI
[2024-01-25 19:58:00,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e33103-2e41-4ea0-a1eb-f1e9de79562c/GCF_025370255.1_ASM2537025v1_genomic.fna.gz --refList GCF_025370255.1_ASM2537025v1_genomic.fna/target_genomes.txt --output GCF_025370255.1_ASM2537025v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:13,106] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:13,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c225733-54a6-473e-a1c6-cb98fab256e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:13,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c225733-54a6-473e-a1c6-cb98fab256e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:13,116] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:58:13,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:58:13,116] [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
Shewanella aestuarii	strain=JCM 17801	GCA_014647215.1	1028752	1028752	type	True	88.4172	1124	1389	95	below_threshold
Shewanella aestuarii	strain=JCM 17801	GCA_023283685.1	1028752	1028752	type	True	88.4129	1110	1389	95	below_threshold
Shewanella glacialimarina	strain=TZS-4	GCA_020511155.1	2590884	2590884	type	True	82.0858	866	1389	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	79.6554	501	1389	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	79.6359	481	1389	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	79.6207	510	1389	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	79.5955	485	1389	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	79.554	479	1389	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	79.5351	489	1389	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	79.511	482	1389	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	79.4664	490	1389	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	79.4364	470	1389	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	79.408	477	1389	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	79.3785	472	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:13,117] [INFO] DFAST Taxonomy check result was written to GCF_025370255.1_ASM2537025v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:13,118] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:13,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:13,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c225733-54a6-473e-a1c6-cb98fab256e9/dqc_reference/checkm_data
[2024-01-25 19:58:13,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:13,162] [INFO] Task started: CheckM
[2024-01-25 19:58:13,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025370255.1_ASM2537025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025370255.1_ASM2537025v1_genomic.fna/checkm_input GCF_025370255.1_ASM2537025v1_genomic.fna/checkm_result
[2024-01-25 19:58:40,819] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:40,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:40,837] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:40,837] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:40,838] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025370255.1_ASM2537025v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:40,838] [INFO] Task started: Blastn
[2024-01-25 19:58:40,838] [INFO] Running command: blastn -query GCF_025370255.1_ASM2537025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c225733-54a6-473e-a1c6-cb98fab256e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025370255.1_ASM2537025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:41,909] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:41,912] [INFO] Selected 16 target genomes.
[2024-01-25 19:58:41,912] [INFO] Target genome list was writen to GCF_025370255.1_ASM2537025v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:41,927] [INFO] Task started: fastANI
[2024-01-25 19:58:41,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e33103-2e41-4ea0-a1eb-f1e9de79562c/GCF_025370255.1_ASM2537025v1_genomic.fna.gz --refList GCF_025370255.1_ASM2537025v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025370255.1_ASM2537025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:56,415] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:56,425] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:58:56,425] [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_014647215.1	s__Shewanella aestuarii	88.4195	1124	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011765625.1	s__Shewanella aestuarii_A	80.2604	641	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648035.1	s__Shewanella algicola	79.737	492	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	79.6989	490	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_010092445.1	s__Shewanella sp002836315	79.6382	493	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.47	98.34	0.91	0.90	4	-
GCF_009828585.1	s__Shewanella litoralis	79.6064	509	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648295.1	s__Shewanella saliphila	79.5696	478	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014164505.1	s__Shewanella sp014164505	79.5506	404	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641855.1	s__Shewanella inventionis	79.5239	488	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648315.1	s__Shewanella ulleungensis	79.4912	483	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797885.1	s__Shewanella vesiculosa	79.4364	470	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.53	98.48	0.92	0.86	17	-
GCF_003855155.1	s__Shewanella sp002836275	79.0955	473	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.14	98.29	0.96	0.92	3	-
GCF_006385555.1	s__Shewanella polaris	79.0205	506	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_000013765.1	s__Shewanella denitrificans	78.9971	280	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221465.1	s__Shewanella intestini	78.5603	340	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006494715.1	s__Shewanella sp006494715	77.7657	182	1389	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:56,427] [INFO] GTDB search result was written to GCF_025370255.1_ASM2537025v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:56,427] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:56,430] [INFO] DFAST_QC result json was written to GCF_025370255.1_ASM2537025v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:56,431] [INFO] DFAST_QC completed!
[2024-01-25 19:58:56,431] [INFO] Total running time: 0h1m6s