[2024-01-25 18:10:20,945] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:20,946] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:20,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg94921f98-faee-46b5-b6f3-c0f8b932c7c8/dqc_reference
[2024-01-25 18:10:22,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:22,096] [INFO] Task started: Prodigal
[2024-01-25 18:10:22,096] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0fbad42-b3fa-4e7f-8e7b-5f4c2efcc7b0/GCF_020421205.1_ASM2042120v1_genomic.fna.gz | prodigal -d GCF_020421205.1_ASM2042120v1_genomic.fna/cds.fna -a GCF_020421205.1_ASM2042120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:47,073] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:47,073] [INFO] Task started: HMMsearch
[2024-01-25 18:10:47,073] [INFO] Running command: hmmsearch --tblout GCF_020421205.1_ASM2042120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94921f98-faee-46b5-b6f3-c0f8b932c7c8/dqc_reference/reference_markers.hmm GCF_020421205.1_ASM2042120v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:47,310] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:47,312] [INFO] Found 6/6 markers.
[2024-01-25 18:10:47,352] [INFO] Query marker FASTA was written to GCF_020421205.1_ASM2042120v1_genomic.fna/markers.fasta
[2024-01-25 18:10:47,352] [INFO] Task started: Blastn
[2024-01-25 18:10:47,352] [INFO] Running command: blastn -query GCF_020421205.1_ASM2042120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94921f98-faee-46b5-b6f3-c0f8b932c7c8/dqc_reference/reference_markers.fasta -out GCF_020421205.1_ASM2042120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:47,934] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:47,938] [INFO] Selected 16 target genomes.
[2024-01-25 18:10:47,938] [INFO] Target genome list was writen to GCF_020421205.1_ASM2042120v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:47,944] [INFO] Task started: fastANI
[2024-01-25 18:10:47,944] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fbad42-b3fa-4e7f-8e7b-5f4c2efcc7b0/GCF_020421205.1_ASM2042120v1_genomic.fna.gz --refList GCF_020421205.1_ASM2042120v1_genomic.fna/target_genomes.txt --output GCF_020421205.1_ASM2042120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:08,186] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:08,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94921f98-faee-46b5-b6f3-c0f8b932c7c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:08,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94921f98-faee-46b5-b6f3-c0f8b932c7c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:08,197] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:11:08,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:11:08,197] [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
Hymenobacter rigui	strain=KCTC 12533	GCA_003944715.1	334424	334424	type	True	86.0019	1308	1711	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	84.5359	1235	1711	95	below_threshold
Hymenobacter perfusus	strain=LMG 26000	GCA_003944765.1	1236770	1236770	type	True	83.9124	1217	1711	95	below_threshold
Hymenobacter swuensis	strain=DY53	GCA_000576555.1	1446467	1446467	type	True	83.4811	1199	1711	95	below_threshold
Hymenobacter piscis	strain=NST-14	GCA_018760735.1	2839984	2839984	type	True	82.8392	1043	1711	95	below_threshold
Hymenobacter glacieicola	strain=CGMCC 1.12990	GCA_014640315.1	1562124	1562124	type	True	81.8045	1038	1711	95	below_threshold
Hymenobacter psychrotolerans	strain=DSM 18569	GCA_900142395.1	344998	344998	type	True	81.4259	904	1711	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	81.3195	938	1711	95	below_threshold
Hymenobacter sediminis	strain=ELS1360	GCA_003231285.1	2218621	2218621	type	True	81.2697	978	1711	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	81.1581	892	1711	95	below_threshold
Hymenobacter aquaticus	strain=JCM 31653	GCA_004765605.1	1867101	1867101	type	True	80.8046	937	1711	95	below_threshold
Hymenobacter fodinae	strain=92R-1	GCA_004745825.1	2510796	2510796	type	True	80.2	900	1711	95	below_threshold
Hymenobacter telluris	strain=BT186	GCA_017313265.1	2816474	2816474	type	True	80.1757	900	1711	95	below_threshold
Hymenobacter wooponensis	strain=JCM 19491	GCA_004745865.1	1525360	1525360	type	True	79.9384	857	1711	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	79.9176	856	1711	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	79.1863	709	1711	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:08,198] [INFO] DFAST Taxonomy check result was written to GCF_020421205.1_ASM2042120v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:08,199] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:08,199] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:08,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94921f98-faee-46b5-b6f3-c0f8b932c7c8/dqc_reference/checkm_data
[2024-01-25 18:11:08,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:08,252] [INFO] Task started: CheckM
[2024-01-25 18:11:08,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020421205.1_ASM2042120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020421205.1_ASM2042120v1_genomic.fna/checkm_input GCF_020421205.1_ASM2042120v1_genomic.fna/checkm_result
[2024-01-25 18:12:12,184] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:12,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:12,201] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:12,202] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:12,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020421205.1_ASM2042120v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:12,203] [INFO] Task started: Blastn
[2024-01-25 18:12:12,203] [INFO] Running command: blastn -query GCF_020421205.1_ASM2042120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94921f98-faee-46b5-b6f3-c0f8b932c7c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_020421205.1_ASM2042120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:13,042] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:13,045] [INFO] Selected 14 target genomes.
[2024-01-25 18:12:13,045] [INFO] Target genome list was writen to GCF_020421205.1_ASM2042120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:13,054] [INFO] Task started: fastANI
[2024-01-25 18:12:13,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0fbad42-b3fa-4e7f-8e7b-5f4c2efcc7b0/GCF_020421205.1_ASM2042120v1_genomic.fna.gz --refList GCF_020421205.1_ASM2042120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020421205.1_ASM2042120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:30,234] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:30,243] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:12:30,243] [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_003944715.1	s__Hymenobacter rigui	86.0093	1308	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944705.1	s__Hymenobacter metallilatus	84.5459	1234	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944765.1	s__Hymenobacter perfusus	83.9008	1219	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576555.1	s__Hymenobacter swuensis	83.4719	1199	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018760735.1	s__Hymenobacter sp018760735	82.8444	1042	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199535.1	s__Hymenobacter latericoloratus	82.4441	1086	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000737515.1	s__Hymenobacter sp000737515	82.0482	997	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006352025.1	s__Hymenobacter sp006352025	82.0471	1066	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640315.1	s__Hymenobacter glacieicola	81.8112	1036	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583925.1	s__Hymenobacter rubripertinctus	81.5679	996	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142395.1	s__Hymenobacter psychrotolerans	81.4467	901	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014250515.1	s__Hymenobacter sp014250515	80.4315	794	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313265.1	s__Hymenobacter sp017313265	80.1747	900	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745865.1	s__Hymenobacter wooponensis	79.9266	860	1711	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:30,244] [INFO] GTDB search result was written to GCF_020421205.1_ASM2042120v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:30,245] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:30,248] [INFO] DFAST_QC result json was written to GCF_020421205.1_ASM2042120v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:30,248] [INFO] DFAST_QC completed!
[2024-01-25 18:12:30,248] [INFO] Total running time: 0h2m9s