[2024-01-24 11:51:06,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,946] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg429f08a1-0d78-4997-97d1-b2e5118e1db9/dqc_reference
[2024-01-24 11:51:08,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,178] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,178] [INFO] Running command: gunzip -c /var/lib/cwl/stg86b5a596-b91d-4775-aeb9-cd2a7f952b7d/GCF_014651535.1_ASM1465153v1_genomic.fna.gz | prodigal -d GCF_014651535.1_ASM1465153v1_genomic.fna/cds.fna -a GCF_014651535.1_ASM1465153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:24,928] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:24,928] [INFO] Task started: HMMsearch
[2024-01-24 11:51:24,928] [INFO] Running command: hmmsearch --tblout GCF_014651535.1_ASM1465153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg429f08a1-0d78-4997-97d1-b2e5118e1db9/dqc_reference/reference_markers.hmm GCF_014651535.1_ASM1465153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:25,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:25,256] [INFO] Found 6/6 markers.
[2024-01-24 11:51:25,298] [INFO] Query marker FASTA was written to GCF_014651535.1_ASM1465153v1_genomic.fna/markers.fasta
[2024-01-24 11:51:25,299] [INFO] Task started: Blastn
[2024-01-24 11:51:25,299] [INFO] Running command: blastn -query GCF_014651535.1_ASM1465153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg429f08a1-0d78-4997-97d1-b2e5118e1db9/dqc_reference/reference_markers.fasta -out GCF_014651535.1_ASM1465153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:25,937] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:25,941] [INFO] Selected 19 target genomes.
[2024-01-24 11:51:25,941] [INFO] Target genome list was writen to GCF_014651535.1_ASM1465153v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:25,964] [INFO] Task started: fastANI
[2024-01-24 11:51:25,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg86b5a596-b91d-4775-aeb9-cd2a7f952b7d/GCF_014651535.1_ASM1465153v1_genomic.fna.gz --refList GCF_014651535.1_ASM1465153v1_genomic.fna/target_genomes.txt --output GCF_014651535.1_ASM1465153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:37,713] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:37,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg429f08a1-0d78-4997-97d1-b2e5118e1db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:37,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg429f08a1-0d78-4997-97d1-b2e5118e1db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:37,728] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:37,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:37,729] [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
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	100.0	1368	1371	95	conclusive
Salinimicrobium oceani	strain=J15B91	GCA_012037645.1	2722702	2722702	type	True	78.5014	254	1371	95	below_threshold
Salinimicrobium catena	strain=CGMCC 1.6101	GCA_900102915.1	390640	390640	type	True	77.9532	252	1371	95	below_threshold
Salinimicrobium catena	strain=DSM 23553	GCA_900107495.1	390640	390640	type	True	77.9327	257	1371	95	below_threshold
Salinimicrobium sediminis	strain=CGMCC 1.12641	GCA_900215295.1	1343891	1343891	type	True	77.6441	290	1371	95	below_threshold
Salinimicrobium xinjiangense	strain=DSM 19287	GCA_000423585.1	438596	438596	type	True	77.6395	286	1371	95	below_threshold
Salinimicrobium terrae	strain=DSM 17865	GCA_000424665.1	470866	470866	type	True	77.5173	295	1371	95	below_threshold
Gramella fulva	strain=SH35	GCA_003024155.1	2126553	2126553	type	True	77.2487	175	1371	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	77.202	221	1371	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	77.1828	200	1371	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	76.9929	160	1371	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	76.7803	153	1371	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	76.2467	62	1371	95	below_threshold
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	75.4717	54	1371	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:37,731] [INFO] DFAST Taxonomy check result was written to GCF_014651535.1_ASM1465153v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:37,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:37,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:37,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg429f08a1-0d78-4997-97d1-b2e5118e1db9/dqc_reference/checkm_data
[2024-01-24 11:51:37,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:37,779] [INFO] Task started: CheckM
[2024-01-24 11:51:37,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651535.1_ASM1465153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651535.1_ASM1465153v1_genomic.fna/checkm_input GCF_014651535.1_ASM1465153v1_genomic.fna/checkm_result
[2024-01-24 11:52:28,704] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:28,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:28,731] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:28,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:28,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651535.1_ASM1465153v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:28,732] [INFO] Task started: Blastn
[2024-01-24 11:52:28,732] [INFO] Running command: blastn -query GCF_014651535.1_ASM1465153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg429f08a1-0d78-4997-97d1-b2e5118e1db9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651535.1_ASM1465153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:29,537] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:29,541] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:29,541] [INFO] Target genome list was writen to GCF_014651535.1_ASM1465153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:29,576] [INFO] Task started: fastANI
[2024-01-24 11:52:29,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg86b5a596-b91d-4775-aeb9-cd2a7f952b7d/GCF_014651535.1_ASM1465153v1_genomic.fna.gz --refList GCF_014651535.1_ASM1465153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651535.1_ASM1465153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:37,856] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:37,879] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:37,879] [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_014651535.1	s__Salinimicrobium marinum	100.0	1368	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012038135.1	s__Salinimicrobium sp012038135	78.0913	287	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102915.1	s__Salinimicrobium catena	77.9577	251	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007993795.1	s__Gillisia arcticum	77.8927	190	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423585.1	s__Salinimicrobium xinjiangense	77.6453	287	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215295.1	s__Salinimicrobium sediminis	77.6218	290	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424665.1	s__Salinimicrobium terrae	77.5284	294	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024155.1	s__Gramella fulva	77.2487	175	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	77.2025	222	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_016236915.1	s__Salegentibacter maritimus	76.9929	160	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCA_002715485.1	s__Aequorivita sp002715485	76.7932	59	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCF_003054225.1	s__Gramella gaetbulicola	76.7768	152	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	76.4304	67	1371	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:37,881] [INFO] GTDB search result was written to GCF_014651535.1_ASM1465153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:37,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:37,885] [INFO] DFAST_QC result json was written to GCF_014651535.1_ASM1465153v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:37,885] [INFO] DFAST_QC completed!
[2024-01-24 11:52:37,885] [INFO] Total running time: 0h1m31s