[2024-01-24 14:55:08,615] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgb923cc62-9136-4413-955e-a0f073a5af68/dqc_reference
[2024-01-24 14:55:10,163] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,164] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,164] [INFO] Running command: gunzip -c /var/lib/cwl/stg2106af7b-1c74-4c12-a800-c8f244fe23b6/GCF_003254665.1_ASM325466v1_genomic.fna.gz | prodigal -d GCF_003254665.1_ASM325466v1_genomic.fna/cds.fna -a GCF_003254665.1_ASM325466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:23,001] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:23,002] [INFO] Task started: HMMsearch
[2024-01-24 14:55:23,002] [INFO] Running command: hmmsearch --tblout GCF_003254665.1_ASM325466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb923cc62-9136-4413-955e-a0f073a5af68/dqc_reference/reference_markers.hmm GCF_003254665.1_ASM325466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:23,272] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:23,273] [INFO] Found 6/6 markers.
[2024-01-24 14:55:23,311] [INFO] Query marker FASTA was written to GCF_003254665.1_ASM325466v1_genomic.fna/markers.fasta
[2024-01-24 14:55:23,311] [INFO] Task started: Blastn
[2024-01-24 14:55:23,311] [INFO] Running command: blastn -query GCF_003254665.1_ASM325466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb923cc62-9136-4413-955e-a0f073a5af68/dqc_reference/reference_markers.fasta -out GCF_003254665.1_ASM325466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:24,281] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:24,285] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:24,285] [INFO] Target genome list was writen to GCF_003254665.1_ASM325466v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:24,293] [INFO] Task started: fastANI
[2024-01-24 14:55:24,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg2106af7b-1c74-4c12-a800-c8f244fe23b6/GCF_003254665.1_ASM325466v1_genomic.fna.gz --refList GCF_003254665.1_ASM325466v1_genomic.fna/target_genomes.txt --output GCF_003254665.1_ASM325466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:39,459] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:39,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb923cc62-9136-4413-955e-a0f073a5af68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:39,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb923cc62-9136-4413-955e-a0f073a5af68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:39,477] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:39,477] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:39,478] [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
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	100.0	1432	1433	95	conclusive
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	90.5444	1195	1433	95	below_threshold
Halomonas bachuensis	strain=DX6	GCA_011742165.1	2717286	2717286	type	True	87.6536	1127	1433	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	87.5518	1147	1433	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	87.5128	1185	1433	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	87.3894	1164	1433	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	86.3582	1038	1433	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	86.2936	1136	1433	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	85.4868	1009	1433	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	85.359	1024	1433	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	82.0077	799	1433	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	81.5766	663	1433	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	80.4026	592	1433	95	below_threshold
Halotalea alkalilenta	strain=DSM 17697	GCA_000621205.1	376489	376489	type	True	78.8623	349	1433	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	77.9919	371	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:39,479] [INFO] DFAST Taxonomy check result was written to GCF_003254665.1_ASM325466v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:39,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:39,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:39,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb923cc62-9136-4413-955e-a0f073a5af68/dqc_reference/checkm_data
[2024-01-24 14:55:39,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:39,530] [INFO] Task started: CheckM
[2024-01-24 14:55:39,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254665.1_ASM325466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254665.1_ASM325466v1_genomic.fna/checkm_input GCF_003254665.1_ASM325466v1_genomic.fna/checkm_result
[2024-01-24 14:56:21,307] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:21,309] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:21,339] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:21,339] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:21,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254665.1_ASM325466v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:21,340] [INFO] Task started: Blastn
[2024-01-24 14:56:21,340] [INFO] Running command: blastn -query GCF_003254665.1_ASM325466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb923cc62-9136-4413-955e-a0f073a5af68/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254665.1_ASM325466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:23,117] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:23,123] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:23,124] [INFO] Target genome list was writen to GCF_003254665.1_ASM325466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:23,135] [INFO] Task started: fastANI
[2024-01-24 14:56:23,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg2106af7b-1c74-4c12-a800-c8f244fe23b6/GCF_003254665.1_ASM325466v1_genomic.fna.gz --refList GCF_003254665.1_ASM325466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254665.1_ASM325466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:35,853] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:35,866] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:35,866] [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_003254665.1	s__Halomonas lactosivorans	100.0	1432	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015992245.1	s__Halomonas sp015992245	90.5197	1190	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
GCF_011742165.1	s__Halomonas bachuensis	87.6438	1128	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017868935.1	s__Halomonas sp017868935	87.522	1184	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834345.1	s__Halomonas sp009834345	87.3838	1165	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014931605.1	s__Halomonas sp014931605	86.9164	1150	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011742915.1	s__Halomonas desiderata	86.9149	1102	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.30	98.24	0.88	0.88	3	-
GCF_013697085.1	s__Halomonas kenyensis	85.3625	1023	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336675.1	s__Halomonas montanilacus	83.471	985	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008298015.1	s__Salinicola sp008298015	79.0399	433	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002179555.1	s__Salinicola salarius_A	79.0062	468	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652715.1	s__Salinicola rhizosphaerae	78.6433	403	1433	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:35,868] [INFO] GTDB search result was written to GCF_003254665.1_ASM325466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:35,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:35,871] [INFO] DFAST_QC result json was written to GCF_003254665.1_ASM325466v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:35,871] [INFO] DFAST_QC completed!
[2024-01-24 14:56:35,872] [INFO] Total running time: 0h1m27s