[2024-01-24 14:22:04,467] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg254e9db6-914b-4bc6-aca6-632556a9c1db/dqc_reference
[2024-01-24 14:22:05,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,810] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,810] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd11bda7-37de-41a0-9a24-33930d848eb1/GCF_019312595.1_ASM1931259v1_genomic.fna.gz | prodigal -d GCF_019312595.1_ASM1931259v1_genomic.fna/cds.fna -a GCF_019312595.1_ASM1931259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:17,431] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:17,432] [INFO] Task started: HMMsearch
[2024-01-24 14:22:17,432] [INFO] Running command: hmmsearch --tblout GCF_019312595.1_ASM1931259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg254e9db6-914b-4bc6-aca6-632556a9c1db/dqc_reference/reference_markers.hmm GCF_019312595.1_ASM1931259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:17,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:17,726] [INFO] Found 6/6 markers.
[2024-01-24 14:22:17,769] [INFO] Query marker FASTA was written to GCF_019312595.1_ASM1931259v1_genomic.fna/markers.fasta
[2024-01-24 14:22:17,770] [INFO] Task started: Blastn
[2024-01-24 14:22:17,770] [INFO] Running command: blastn -query GCF_019312595.1_ASM1931259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg254e9db6-914b-4bc6-aca6-632556a9c1db/dqc_reference/reference_markers.fasta -out GCF_019312595.1_ASM1931259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:18,558] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:18,562] [INFO] Selected 28 target genomes.
[2024-01-24 14:22:18,563] [INFO] Target genome list was writen to GCF_019312595.1_ASM1931259v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:18,574] [INFO] Task started: fastANI
[2024-01-24 14:22:18,574] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd11bda7-37de-41a0-9a24-33930d848eb1/GCF_019312595.1_ASM1931259v1_genomic.fna.gz --refList GCF_019312595.1_ASM1931259v1_genomic.fna/target_genomes.txt --output GCF_019312595.1_ASM1931259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:35,517] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:35,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg254e9db6-914b-4bc6-aca6-632556a9c1db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:35,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg254e9db6-914b-4bc6-aca6-632556a9c1db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:35,526] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:35,527] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:35,527] [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
Zhongshania aliphaticivorans	strain=SM-2	GCA_001586255.1	1470434	1470434	type	True	79.0939	361	1411	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	78.9574	349	1411	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	78.8097	347	1411	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.7949	134	1411	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	77.5138	157	1411	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.1005	154	1411	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	76.9983	152	1411	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	76.9574	127	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:35,528] [INFO] DFAST Taxonomy check result was written to GCF_019312595.1_ASM1931259v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:35,529] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:35,529] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:35,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg254e9db6-914b-4bc6-aca6-632556a9c1db/dqc_reference/checkm_data
[2024-01-24 14:22:35,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:35,577] [INFO] Task started: CheckM
[2024-01-24 14:22:35,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019312595.1_ASM1931259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019312595.1_ASM1931259v1_genomic.fna/checkm_input GCF_019312595.1_ASM1931259v1_genomic.fna/checkm_result
[2024-01-24 14:23:11,720] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:11,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:11,745] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:11,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:11,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019312595.1_ASM1931259v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:11,747] [INFO] Task started: Blastn
[2024-01-24 14:23:11,747] [INFO] Running command: blastn -query GCF_019312595.1_ASM1931259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg254e9db6-914b-4bc6-aca6-632556a9c1db/dqc_reference/reference_markers_gtdb.fasta -out GCF_019312595.1_ASM1931259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:12,896] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:12,900] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:12,901] [INFO] Target genome list was writen to GCF_019312595.1_ASM1931259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:12,912] [INFO] Task started: fastANI
[2024-01-24 14:23:12,912] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd11bda7-37de-41a0-9a24-33930d848eb1/GCF_019312595.1_ASM1931259v1_genomic.fna.gz --refList GCF_019312595.1_ASM1931259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019312595.1_ASM1931259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:21,294] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:21,307] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:21,307] [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
GCA_018067195.1	s__Marortus sp018067195	95.3186	990	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018066965.1	s__Marortus sp018066965	82.3002	621	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705855.1	s__Marortus aliphaticivorans_B	81.2637	635	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002915595.1	s__Marortus luteolus	80.864	613	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	79.417	457	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001586255.1	s__Zhongshania aliphaticivorans	79.0896	360	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	-
GCF_014202945.1	s__Zhongshania antarctica	78.9589	348	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014705705.1	s__KMU-158 sp014705705	77.1005	154	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420325.1	s__Spongiibacter tropicus	76.9983	152	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
GCA_002415025.1	s__Litorivivens sp002415025	76.439	62	1411	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Litorivivens	95.0	99.88	99.82	0.96	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:21,309] [INFO] GTDB search result was written to GCF_019312595.1_ASM1931259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:21,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:21,313] [INFO] DFAST_QC result json was written to GCF_019312595.1_ASM1931259v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:21,313] [INFO] DFAST_QC completed!
[2024-01-24 14:23:21,314] [INFO] Total running time: 0h1m17s