[2024-01-24 11:05:03,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg67477daa-284a-40dc-b9df-412ec6be2501/dqc_reference
[2024-01-24 11:05:05,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,765] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg70e172b9-01d3-4fe7-b704-0cab7afbb670/GCF_012037645.1_ASM1203764v1_genomic.fna.gz | prodigal -d GCF_012037645.1_ASM1203764v1_genomic.fna/cds.fna -a GCF_012037645.1_ASM1203764v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:20,159] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:20,159] [INFO] Task started: HMMsearch
[2024-01-24 11:05:20,160] [INFO] Running command: hmmsearch --tblout GCF_012037645.1_ASM1203764v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67477daa-284a-40dc-b9df-412ec6be2501/dqc_reference/reference_markers.hmm GCF_012037645.1_ASM1203764v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:20,477] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:20,479] [INFO] Found 6/6 markers.
[2024-01-24 11:05:20,530] [INFO] Query marker FASTA was written to GCF_012037645.1_ASM1203764v1_genomic.fna/markers.fasta
[2024-01-24 11:05:20,531] [INFO] Task started: Blastn
[2024-01-24 11:05:20,531] [INFO] Running command: blastn -query GCF_012037645.1_ASM1203764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67477daa-284a-40dc-b9df-412ec6be2501/dqc_reference/reference_markers.fasta -out GCF_012037645.1_ASM1203764v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:21,119] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:21,122] [INFO] Selected 13 target genomes.
[2024-01-24 11:05:21,122] [INFO] Target genome list was writen to GCF_012037645.1_ASM1203764v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:21,127] [INFO] Task started: fastANI
[2024-01-24 11:05:21,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg70e172b9-01d3-4fe7-b704-0cab7afbb670/GCF_012037645.1_ASM1203764v1_genomic.fna.gz --refList GCF_012037645.1_ASM1203764v1_genomic.fna/target_genomes.txt --output GCF_012037645.1_ASM1203764v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:30,028] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:30,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67477daa-284a-40dc-b9df-412ec6be2501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:30,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67477daa-284a-40dc-b9df-412ec6be2501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:30,036] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:30,036] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:30,036] [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 oceani	strain=J15B91	GCA_012037645.1	2722702	2722702	type	True	100.0	1102	1102	95	conclusive
Salinimicrobium xinjiangense	strain=DSM 19287	GCA_000423585.1	438596	438596	type	True	79.9243	563	1102	95	below_threshold
Salinimicrobium sediminis	strain=CGMCC 1.12641	GCA_900215295.1	1343891	1343891	type	True	79.731	534	1102	95	below_threshold
Salinimicrobium terrae	strain=DSM 17865	GCA_000424665.1	470866	470866	type	True	79.3843	442	1102	95	below_threshold
Salinimicrobium catena	strain=CGMCC 1.6101	GCA_900102915.1	390640	390640	type	True	78.5149	318	1102	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	78.429	260	1102	95	below_threshold
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	77.8813	181	1102	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	77.3247	111	1102	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	76.7252	127	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:30,038] [INFO] DFAST Taxonomy check result was written to GCF_012037645.1_ASM1203764v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:30,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:30,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:30,038] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67477daa-284a-40dc-b9df-412ec6be2501/dqc_reference/checkm_data
[2024-01-24 11:05:30,039] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:30,081] [INFO] Task started: CheckM
[2024-01-24 11:05:30,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012037645.1_ASM1203764v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012037645.1_ASM1203764v1_genomic.fna/checkm_input GCF_012037645.1_ASM1203764v1_genomic.fna/checkm_result
[2024-01-24 11:06:12,173] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:12,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 15.34%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2024-01-24 11:06:12,193] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:12,193] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:12,193] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012037645.1_ASM1203764v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:12,194] [INFO] Task started: Blastn
[2024-01-24 11:06:12,194] [INFO] Running command: blastn -query GCF_012037645.1_ASM1203764v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67477daa-284a-40dc-b9df-412ec6be2501/dqc_reference/reference_markers_gtdb.fasta -out GCF_012037645.1_ASM1203764v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:13,102] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:13,104] [INFO] Selected 12 target genomes.
[2024-01-24 11:06:13,104] [INFO] Target genome list was writen to GCF_012037645.1_ASM1203764v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:13,110] [INFO] Task started: fastANI
[2024-01-24 11:06:13,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg70e172b9-01d3-4fe7-b704-0cab7afbb670/GCF_012037645.1_ASM1203764v1_genomic.fna.gz --refList GCF_012037645.1_ASM1203764v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012037645.1_ASM1203764v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:21,245] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:21,253] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:21,253] [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_012038135.1	s__Salinimicrobium sp012038135	80.8352	532	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423585.1	s__Salinimicrobium xinjiangense	79.9244	563	1102	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	79.7055	536	1102	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	79.3732	443	1102	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	78.5328	318	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014651535.1	s__Salinimicrobium marinum	78.4234	261	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006159205.1	s__Gillisia flava	77.8438	183	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006714895.1	s__Gramella sp006714895	77.3893	106	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997295.1	s__Gillisia hiemivivida	76.9634	104	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCF_000023465.1	s__Zunongwangia profunda	76.9199	100	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	99.17	98.44	0.93	0.80	11	-
GCF_900113135.1	s__Salegentibacter agarivorans	76.7091	130	1102	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:21,254] [INFO] GTDB search result was written to GCF_012037645.1_ASM1203764v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:21,255] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:21,257] [INFO] DFAST_QC result json was written to GCF_012037645.1_ASM1203764v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:21,257] [INFO] DFAST_QC completed!
[2024-01-24 11:06:21,258] [INFO] Total running time: 0h1m17s