[2024-01-24 14:42:14,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:42:14,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:42:14,565] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa473130-e16b-4f2b-8b24-f4e67e45a1b8/dqc_reference
[2024-01-24 14:42:15,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:42:15,942] [INFO] Task started: Prodigal
[2024-01-24 14:42:15,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg32471c2e-890c-4249-9747-3a83751e3fb8/GCF_005047595.1_ASM504759v1_genomic.fna.gz | prodigal -d GCF_005047595.1_ASM504759v1_genomic.fna/cds.fna -a GCF_005047595.1_ASM504759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:42:27,302] [INFO] Task succeeded: Prodigal
[2024-01-24 14:42:27,303] [INFO] Task started: HMMsearch
[2024-01-24 14:42:27,303] [INFO] Running command: hmmsearch --tblout GCF_005047595.1_ASM504759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa473130-e16b-4f2b-8b24-f4e67e45a1b8/dqc_reference/reference_markers.hmm GCF_005047595.1_ASM504759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:42:27,601] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:42:27,603] [INFO] Found 6/6 markers.
[2024-01-24 14:42:27,638] [INFO] Query marker FASTA was written to GCF_005047595.1_ASM504759v1_genomic.fna/markers.fasta
[2024-01-24 14:42:27,639] [INFO] Task started: Blastn
[2024-01-24 14:42:27,639] [INFO] Running command: blastn -query GCF_005047595.1_ASM504759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa473130-e16b-4f2b-8b24-f4e67e45a1b8/dqc_reference/reference_markers.fasta -out GCF_005047595.1_ASM504759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:28,377] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:28,381] [INFO] Selected 23 target genomes.
[2024-01-24 14:42:28,381] [INFO] Target genome list was writen to GCF_005047595.1_ASM504759v1_genomic.fna/target_genomes.txt
[2024-01-24 14:42:28,394] [INFO] Task started: fastANI
[2024-01-24 14:42:28,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg32471c2e-890c-4249-9747-3a83751e3fb8/GCF_005047595.1_ASM504759v1_genomic.fna.gz --refList GCF_005047595.1_ASM504759v1_genomic.fna/target_genomes.txt --output GCF_005047595.1_ASM504759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:42:43,188] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:43,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa473130-e16b-4f2b-8b24-f4e67e45a1b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:42:43,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa473130-e16b-4f2b-8b24-f4e67e45a1b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:42:43,211] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:42:43,211] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:42:43,211] [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
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	100.0	1092	1092	95	conclusive
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	78.156	229	1092	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	78.0447	206	1092	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.7811	240	1092	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.7538	249	1092	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	77.7391	212	1092	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	77.7123	259	1092	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.6725	218	1092	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.5936	193	1092	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.5749	219	1092	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.5396	248	1092	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.5357	260	1092	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.5187	286	1092	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.5112	167	1092	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	77.4781	221	1092	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.4696	284	1092	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.4644	217	1092	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.4616	176	1092	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	77.4035	229	1092	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.3866	189	1092	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	77.2916	184	1092	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.2833	264	1092	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	77.235	208	1092	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:42:43,215] [INFO] DFAST Taxonomy check result was written to GCF_005047595.1_ASM504759v1_genomic.fna/tc_result.tsv
[2024-01-24 14:42:43,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:42:43,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:42:43,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa473130-e16b-4f2b-8b24-f4e67e45a1b8/dqc_reference/checkm_data
[2024-01-24 14:42:43,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:42:43,255] [INFO] Task started: CheckM
[2024-01-24 14:42:43,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005047595.1_ASM504759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005047595.1_ASM504759v1_genomic.fna/checkm_input GCF_005047595.1_ASM504759v1_genomic.fna/checkm_result
[2024-01-24 14:43:17,567] [INFO] Task succeeded: CheckM
[2024-01-24 14:43:17,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:43:17,590] [INFO] ===== Completeness check finished =====
[2024-01-24 14:43:17,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:43:17,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005047595.1_ASM504759v1_genomic.fna/markers.fasta)
[2024-01-24 14:43:17,591] [INFO] Task started: Blastn
[2024-01-24 14:43:17,591] [INFO] Running command: blastn -query GCF_005047595.1_ASM504759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa473130-e16b-4f2b-8b24-f4e67e45a1b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_005047595.1_ASM504759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:43:18,546] [INFO] Task succeeded: Blastn
[2024-01-24 14:43:18,551] [INFO] Selected 22 target genomes.
[2024-01-24 14:43:18,551] [INFO] Target genome list was writen to GCF_005047595.1_ASM504759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:43:18,620] [INFO] Task started: fastANI
[2024-01-24 14:43:18,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg32471c2e-890c-4249-9747-3a83751e3fb8/GCF_005047595.1_ASM504759v1_genomic.fna.gz --refList GCF_005047595.1_ASM504759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005047595.1_ASM504759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:43:32,457] [INFO] Task succeeded: fastANI
[2024-01-24 14:43:32,480] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:43:32,480] [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_005047595.1	s__CAU-1491 sp005047595	100.0	1092	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011777505.1	s__CAU-1491 sp011777505	83.2676	758	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	78.5134	290	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006148925.1	s__Algibacter_D aestuarii	78.0553	206	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148645.1	s__Xanthomarina spongicola	78.0147	302	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042715.1	s__Site-B15 sp013042715	77.9697	216	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Site-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.9306	304	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.8933	297	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	77.8889	289	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.8368	314	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259525.1	s__Olleya aquimaris	77.7003	260	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	77.6691	278	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	77.6104	297	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.5516	247	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	77.5244	283	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874335.1	s__MedPE-SWsnd-G2 sp001874335	77.487	180	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MedPE-SWsnd-G2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	77.4639	250	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	77.4621	283	1092	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	77.3549	218	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	77.2194	241	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	77.0671	236	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	76.9399	236	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:43:32,484] [INFO] GTDB search result was written to GCF_005047595.1_ASM504759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:43:32,485] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:43:32,489] [INFO] DFAST_QC result json was written to GCF_005047595.1_ASM504759v1_genomic.fna/dqc_result.json
[2024-01-24 14:43:32,489] [INFO] DFAST_QC completed!
[2024-01-24 14:43:32,490] [INFO] Total running time: 0h1m18s