[2024-01-25 18:57:50,601] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:50,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:50,604] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5abbaca-424e-4eb8-a407-55f83b53b623/dqc_reference
[2024-01-25 18:57:51,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:51,843] [INFO] Task started: Prodigal
[2024-01-25 18:57:51,843] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7e06b28-e74a-4ecc-8a03-8a1d92b5fd5e/GCF_030540765.1_ASM3054076v1_genomic.fna.gz | prodigal -d GCF_030540765.1_ASM3054076v1_genomic.fna/cds.fna -a GCF_030540765.1_ASM3054076v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:58:07,010] [INFO] Task succeeded: Prodigal
[2024-01-25 18:58:07,010] [INFO] Task started: HMMsearch
[2024-01-25 18:58:07,010] [INFO] Running command: hmmsearch --tblout GCF_030540765.1_ASM3054076v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5abbaca-424e-4eb8-a407-55f83b53b623/dqc_reference/reference_markers.hmm GCF_030540765.1_ASM3054076v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:58:07,379] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:58:07,380] [INFO] Found 6/6 markers.
[2024-01-25 18:58:07,431] [INFO] Query marker FASTA was written to GCF_030540765.1_ASM3054076v1_genomic.fna/markers.fasta
[2024-01-25 18:58:07,431] [INFO] Task started: Blastn
[2024-01-25 18:58:07,431] [INFO] Running command: blastn -query GCF_030540765.1_ASM3054076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5abbaca-424e-4eb8-a407-55f83b53b623/dqc_reference/reference_markers.fasta -out GCF_030540765.1_ASM3054076v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:08,096] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:08,099] [INFO] Selected 13 target genomes.
[2024-01-25 18:58:08,099] [INFO] Target genome list was writen to GCF_030540765.1_ASM3054076v1_genomic.fna/target_genomes.txt
[2024-01-25 18:58:08,107] [INFO] Task started: fastANI
[2024-01-25 18:58:08,107] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7e06b28-e74a-4ecc-8a03-8a1d92b5fd5e/GCF_030540765.1_ASM3054076v1_genomic.fna.gz --refList GCF_030540765.1_ASM3054076v1_genomic.fna/target_genomes.txt --output GCF_030540765.1_ASM3054076v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:20,758] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:20,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5abbaca-424e-4eb8-a407-55f83b53b623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:20,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5abbaca-424e-4eb8-a407-55f83b53b623/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:20,768] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:58:20,768] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:58:20,768] [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
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	82.7944	891	1991	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	81.4761	852	1991	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	81.3401	896	1991	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.6277	561	1991	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.4574	456	1991	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.4552	504	1991	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.4281	509	1991	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.3836	427	1991	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.3149	533	1991	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.9354	427	1991	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.6891	285	1991	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.394	296	1991	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.2546	175	1991	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:20,770] [INFO] DFAST Taxonomy check result was written to GCF_030540765.1_ASM3054076v1_genomic.fna/tc_result.tsv
[2024-01-25 18:58:20,771] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:20,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:20,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5abbaca-424e-4eb8-a407-55f83b53b623/dqc_reference/checkm_data
[2024-01-25 18:58:20,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:20,831] [INFO] Task started: CheckM
[2024-01-25 18:58:20,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030540765.1_ASM3054076v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030540765.1_ASM3054076v1_genomic.fna/checkm_input GCF_030540765.1_ASM3054076v1_genomic.fna/checkm_result
[2024-01-25 18:59:05,649] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:05,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:05,677] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:05,677] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:05,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030540765.1_ASM3054076v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:05,678] [INFO] Task started: Blastn
[2024-01-25 18:59:05,678] [INFO] Running command: blastn -query GCF_030540765.1_ASM3054076v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5abbaca-424e-4eb8-a407-55f83b53b623/dqc_reference/reference_markers_gtdb.fasta -out GCF_030540765.1_ASM3054076v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:06,622] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:06,626] [INFO] Selected 11 target genomes.
[2024-01-25 18:59:06,626] [INFO] Target genome list was writen to GCF_030540765.1_ASM3054076v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:06,641] [INFO] Task started: fastANI
[2024-01-25 18:59:06,641] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7e06b28-e74a-4ecc-8a03-8a1d92b5fd5e/GCF_030540765.1_ASM3054076v1_genomic.fna.gz --refList GCF_030540765.1_ASM3054076v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030540765.1_ASM3054076v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:16,702] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:16,710] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:59:16,710] [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_004791695.1	s__Flavivirga rizhaonensis	82.8041	890	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	81.4761	852	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	81.3374	897	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	79.4747	575	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	79.2399	610	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.1945	564	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.6277	561	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	78.5398	403	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.4574	456	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.3759	428	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.3117	535	1991	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:16,711] [INFO] GTDB search result was written to GCF_030540765.1_ASM3054076v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:16,712] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:16,715] [INFO] DFAST_QC result json was written to GCF_030540765.1_ASM3054076v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:16,715] [INFO] DFAST_QC completed!
[2024-01-25 18:59:16,715] [INFO] Total running time: 0h1m26s