[2024-01-24 13:18:32,441] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:32,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:32,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgaee8bcb5-bccd-4d66-9792-870d699e1ac5/dqc_reference
[2024-01-24 13:18:33,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:33,839] [INFO] Task started: Prodigal
[2024-01-24 13:18:33,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg7158c2c4-7f8e-495f-b8ba-cee54d558484/GCF_019740355.2_ASM1974035v2_genomic.fna.gz | prodigal -d GCF_019740355.2_ASM1974035v2_genomic.fna/cds.fna -a GCF_019740355.2_ASM1974035v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:51,818] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:51,818] [INFO] Task started: HMMsearch
[2024-01-24 13:18:51,819] [INFO] Running command: hmmsearch --tblout GCF_019740355.2_ASM1974035v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaee8bcb5-bccd-4d66-9792-870d699e1ac5/dqc_reference/reference_markers.hmm GCF_019740355.2_ASM1974035v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:52,129] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:52,130] [INFO] Found 6/6 markers.
[2024-01-24 13:18:52,169] [INFO] Query marker FASTA was written to GCF_019740355.2_ASM1974035v2_genomic.fna/markers.fasta
[2024-01-24 13:18:52,170] [INFO] Task started: Blastn
[2024-01-24 13:18:52,170] [INFO] Running command: blastn -query GCF_019740355.2_ASM1974035v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaee8bcb5-bccd-4d66-9792-870d699e1ac5/dqc_reference/reference_markers.fasta -out GCF_019740355.2_ASM1974035v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:52,825] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:52,829] [INFO] Selected 25 target genomes.
[2024-01-24 13:18:52,829] [INFO] Target genome list was writen to GCF_019740355.2_ASM1974035v2_genomic.fna/target_genomes.txt
[2024-01-24 13:18:52,844] [INFO] Task started: fastANI
[2024-01-24 13:18:52,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg7158c2c4-7f8e-495f-b8ba-cee54d558484/GCF_019740355.2_ASM1974035v2_genomic.fna.gz --refList GCF_019740355.2_ASM1974035v2_genomic.fna/target_genomes.txt --output GCF_019740355.2_ASM1974035v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:11,710] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:11,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaee8bcb5-bccd-4d66-9792-870d699e1ac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:11,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaee8bcb5-bccd-4d66-9792-870d699e1ac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:11,719] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:11,719] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:11,719] [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
Lishizhenia tianjinensis	strain=CGMCC 1.7005	GCA_900116425.1	477690	477690	type	True	76.7141	53	1455	95	below_threshold
Putridiphycobacter roseus	strain=SM1701	GCA_003234935.1	2219161	2219161	type	True	76.3123	85	1455	95	below_threshold
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	76.1323	122	1455	95	below_threshold
Crocinitomix algicola	strain=0182	GCA_001661595.2	1740263	1740263	type	True	76.0956	86	1455	95	below_threshold
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.0608	53	1455	95	below_threshold
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	75.8518	54	1455	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	75.7634	58	1455	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:11,721] [INFO] DFAST Taxonomy check result was written to GCF_019740355.2_ASM1974035v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:11,722] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:11,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:11,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaee8bcb5-bccd-4d66-9792-870d699e1ac5/dqc_reference/checkm_data
[2024-01-24 13:19:11,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:11,769] [INFO] Task started: CheckM
[2024-01-24 13:19:11,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019740355.2_ASM1974035v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019740355.2_ASM1974035v2_genomic.fna/checkm_input GCF_019740355.2_ASM1974035v2_genomic.fna/checkm_result
[2024-01-24 13:20:04,153] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:04,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:04,173] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:04,174] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:04,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019740355.2_ASM1974035v2_genomic.fna/markers.fasta)
[2024-01-24 13:20:04,175] [INFO] Task started: Blastn
[2024-01-24 13:20:04,175] [INFO] Running command: blastn -query GCF_019740355.2_ASM1974035v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgaee8bcb5-bccd-4d66-9792-870d699e1ac5/dqc_reference/reference_markers_gtdb.fasta -out GCF_019740355.2_ASM1974035v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:05,032] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:05,036] [INFO] Selected 27 target genomes.
[2024-01-24 13:20:05,036] [INFO] Target genome list was writen to GCF_019740355.2_ASM1974035v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:05,110] [INFO] Task started: fastANI
[2024-01-24 13:20:05,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg7158c2c4-7f8e-495f-b8ba-cee54d558484/GCF_019740355.2_ASM1974035v2_genomic.fna.gz --refList GCF_019740355.2_ASM1974035v2_genomic.fna/target_genomes_gtdb.txt --output GCF_019740355.2_ASM1974035v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:19,115] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:19,125] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:20:19,125] [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_014762645.1	s__JABURP01 sp014762645	77.2769	231	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JABURP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116425.1	s__Lishizhenia tianjinensis	76.7141	53	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Lishizhenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709005.1	s__JADJGJ01 sp016709005	76.6091	101	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	98.05	97.64	0.91	0.88	3	-
GCA_016192075.1	s__JADJGJ01 sp016192075	76.491	70	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478225.1	s__Crocinitomix sp905478225	76.433	93	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	76.3367	54	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234935.1	s__Putridiphycobacter roseus	76.3123	85	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621625.1	s__Crocinitomix catalasitica	76.1323	122	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661595.2	s__Crocinitomix algicola	76.0956	86	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138735.1	s__Crocinitomix sp013138735	76.0913	119	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662905.1	s__Putridiphycobacter sp015662905	75.9636	67	1455	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:19,127] [INFO] GTDB search result was written to GCF_019740355.2_ASM1974035v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:19,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:19,132] [INFO] DFAST_QC result json was written to GCF_019740355.2_ASM1974035v2_genomic.fna/dqc_result.json
[2024-01-24 13:20:19,132] [INFO] DFAST_QC completed!
[2024-01-24 13:20:19,132] [INFO] Total running time: 0h1m47s