[2024-01-24 13:55:58,099] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:58,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:58,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b0231a7-2341-4982-91f8-e02faf09bfe4/dqc_reference
[2024-01-24 13:55:59,363] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,363] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,364] [INFO] Running command: gunzip -c /var/lib/cwl/stgefa9967b-f5b6-4f6e-b2a9-14433b173d35/GCF_013376415.1_ASM1337641v1_genomic.fna.gz | prodigal -d GCF_013376415.1_ASM1337641v1_genomic.fna/cds.fna -a GCF_013376415.1_ASM1337641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:20,272] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:20,273] [INFO] Task started: HMMsearch
[2024-01-24 13:56:20,273] [INFO] Running command: hmmsearch --tblout GCF_013376415.1_ASM1337641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b0231a7-2341-4982-91f8-e02faf09bfe4/dqc_reference/reference_markers.hmm GCF_013376415.1_ASM1337641v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:20,534] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:20,535] [INFO] Found 6/6 markers.
[2024-01-24 13:56:20,573] [INFO] Query marker FASTA was written to GCF_013376415.1_ASM1337641v1_genomic.fna/markers.fasta
[2024-01-24 13:56:20,574] [INFO] Task started: Blastn
[2024-01-24 13:56:20,574] [INFO] Running command: blastn -query GCF_013376415.1_ASM1337641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b0231a7-2341-4982-91f8-e02faf09bfe4/dqc_reference/reference_markers.fasta -out GCF_013376415.1_ASM1337641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:21,198] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:21,205] [INFO] Selected 9 target genomes.
[2024-01-24 13:56:21,206] [INFO] Target genome list was writen to GCF_013376415.1_ASM1337641v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:21,213] [INFO] Task started: fastANI
[2024-01-24 13:56:21,213] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa9967b-f5b6-4f6e-b2a9-14433b173d35/GCF_013376415.1_ASM1337641v1_genomic.fna.gz --refList GCF_013376415.1_ASM1337641v1_genomic.fna/target_genomes.txt --output GCF_013376415.1_ASM1337641v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:28,318] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:28,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b0231a7-2341-4982-91f8-e02faf09bfe4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:28,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b0231a7-2341-4982-91f8-e02faf09bfe4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:28,331] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:28,331] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:56:28,331] [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
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	100.0	1249	1251	95	inconclusive
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	96.89	1106	1251	95	inconclusive
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	89.8251	1025	1251	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	85.0966	891	1251	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	85.0663	901	1251	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	81.7439	725	1251	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	78.5542	480	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:28,332] [INFO] DFAST Taxonomy check result was written to GCF_013376415.1_ASM1337641v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:28,333] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:28,333] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:28,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b0231a7-2341-4982-91f8-e02faf09bfe4/dqc_reference/checkm_data
[2024-01-24 13:56:28,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:28,371] [INFO] Task started: CheckM
[2024-01-24 13:56:28,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013376415.1_ASM1337641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013376415.1_ASM1337641v1_genomic.fna/checkm_input GCF_013376415.1_ASM1337641v1_genomic.fna/checkm_result
[2024-01-24 13:57:27,262] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:27,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:27,286] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:27,287] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:27,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013376415.1_ASM1337641v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:27,288] [INFO] Task started: Blastn
[2024-01-24 13:57:27,288] [INFO] Running command: blastn -query GCF_013376415.1_ASM1337641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b0231a7-2341-4982-91f8-e02faf09bfe4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013376415.1_ASM1337641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:28,181] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:28,184] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:28,184] [INFO] Target genome list was writen to GCF_013376415.1_ASM1337641v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:28,197] [INFO] Task started: fastANI
[2024-01-24 13:57:28,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa9967b-f5b6-4f6e-b2a9-14433b173d35/GCF_013376415.1_ASM1337641v1_genomic.fna.gz --refList GCF_013376415.1_ASM1337641v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013376415.1_ASM1337641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:37,339] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:37,354] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:37,354] [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_003057865.1	s__Muricauda brasiliensis	96.89	1106	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	conclusive
GCF_017313785.1	s__Muricauda sp002711825	89.8251	1025	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_011068285.1	s__Muricauda sp011068285	85.0624	901	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	82.8306	761	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	82.5943	795	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCA_013911645.1	s__Muricauda sp013911645	81.9357	754	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	81.8524	702	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	81.7483	724	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	81.5022	743	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992675.1	s__Muricauda aquimarina	80.8565	613	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	78.5985	423	1251	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:37,356] [INFO] GTDB search result was written to GCF_013376415.1_ASM1337641v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:37,357] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:37,360] [INFO] DFAST_QC result json was written to GCF_013376415.1_ASM1337641v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:37,360] [INFO] DFAST_QC completed!
[2024-01-24 13:57:37,360] [INFO] Total running time: 0h1m39s