[2024-01-24 14:30:33,136] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:33,140] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:33,140] [INFO] DQC Reference Directory: /var/lib/cwl/stg5485314a-c01a-4dcd-9adf-dfb323e3a382/dqc_reference
[2024-01-24 14:30:34,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:34,536] [INFO] Task started: Prodigal
[2024-01-24 14:30:34,536] [INFO] Running command: gunzip -c /var/lib/cwl/stg14146412-927b-43af-9f51-52727fdaac57/GCF_004804355.1_ASM480435v1_genomic.fna.gz | prodigal -d GCF_004804355.1_ASM480435v1_genomic.fna/cds.fna -a GCF_004804355.1_ASM480435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:46,331] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:46,331] [INFO] Task started: HMMsearch
[2024-01-24 14:30:46,331] [INFO] Running command: hmmsearch --tblout GCF_004804355.1_ASM480435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5485314a-c01a-4dcd-9adf-dfb323e3a382/dqc_reference/reference_markers.hmm GCF_004804355.1_ASM480435v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:46,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:46,620] [INFO] Found 6/6 markers.
[2024-01-24 14:30:46,652] [INFO] Query marker FASTA was written to GCF_004804355.1_ASM480435v1_genomic.fna/markers.fasta
[2024-01-24 14:30:46,652] [INFO] Task started: Blastn
[2024-01-24 14:30:46,652] [INFO] Running command: blastn -query GCF_004804355.1_ASM480435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5485314a-c01a-4dcd-9adf-dfb323e3a382/dqc_reference/reference_markers.fasta -out GCF_004804355.1_ASM480435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:47,371] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:47,375] [INFO] Selected 21 target genomes.
[2024-01-24 14:30:47,375] [INFO] Target genome list was writen to GCF_004804355.1_ASM480435v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:47,384] [INFO] Task started: fastANI
[2024-01-24 14:30:47,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg14146412-927b-43af-9f51-52727fdaac57/GCF_004804355.1_ASM480435v1_genomic.fna.gz --refList GCF_004804355.1_ASM480435v1_genomic.fna/target_genomes.txt --output GCF_004804355.1_ASM480435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:03,231] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:03,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5485314a-c01a-4dcd-9adf-dfb323e3a382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:03,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5485314a-c01a-4dcd-9adf-dfb323e3a382/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:03,249] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:03,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:03,249] [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
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	100.0	1134	1134	95	conclusive
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	79.3752	499	1134	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.6546	446	1134	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.6015	378	1134	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.5735	383	1134	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.48	357	1134	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.48	357	1134	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.4514	360	1134	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.3567	367	1134	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	78.3484	310	1134	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	78.1811	301	1134	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.1511	339	1134	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.0062	344	1134	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.969	286	1134	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	77.955	312	1134	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.8197	136	1134	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.8116	314	1134	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.7833	175	1134	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	77.6806	306	1134	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.6677	225	1134	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.3427	141	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:03,251] [INFO] DFAST Taxonomy check result was written to GCF_004804355.1_ASM480435v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:03,252] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:03,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:03,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5485314a-c01a-4dcd-9adf-dfb323e3a382/dqc_reference/checkm_data
[2024-01-24 14:31:03,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:03,294] [INFO] Task started: CheckM
[2024-01-24 14:31:03,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004804355.1_ASM480435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004804355.1_ASM480435v1_genomic.fna/checkm_input GCF_004804355.1_ASM480435v1_genomic.fna/checkm_result
[2024-01-24 14:31:42,560] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:42,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:42,584] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:42,585] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:42,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004804355.1_ASM480435v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:42,586] [INFO] Task started: Blastn
[2024-01-24 14:31:42,586] [INFO] Running command: blastn -query GCF_004804355.1_ASM480435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5485314a-c01a-4dcd-9adf-dfb323e3a382/dqc_reference/reference_markers_gtdb.fasta -out GCF_004804355.1_ASM480435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:43,646] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:43,650] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:43,650] [INFO] Target genome list was writen to GCF_004804355.1_ASM480435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:43,664] [INFO] Task started: fastANI
[2024-01-24 14:31:43,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg14146412-927b-43af-9f51-52727fdaac57/GCF_004804355.1_ASM480435v1_genomic.fna.gz --refList GCF_004804355.1_ASM480435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004804355.1_ASM480435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:56,935] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:56,956] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:56,957] [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_004804355.1	s__Tamlana_C sp004804355	100.0	1134	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014651495.1	s__Algibacter_E mikhailovii	79.3718	497	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.6852	384	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265225.1	s__Tamlana_C fucoidanivorans	78.6413	398	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.6342	448	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.5821	381	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.4514	360	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.4308	373	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	78.3521	368	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.2693	347	1134	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_018860245.1	s__Tamlana_A agarivorans_A	78.2461	315	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	78.1511	339	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	77.997	271	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.9852	346	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.8771	328	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.853	333	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943565.1	s__Tamlana_B sedimentorum	77.7674	288	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	77.4837	183	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:56,959] [INFO] GTDB search result was written to GCF_004804355.1_ASM480435v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:56,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:56,963] [INFO] DFAST_QC result json was written to GCF_004804355.1_ASM480435v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:56,964] [INFO] DFAST_QC completed!
[2024-01-24 14:31:56,964] [INFO] Total running time: 0h1m24s