[2024-01-24 13:49:17,694] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:17,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:17,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg218bf336-dd62-4ee3-b2c7-2d03c61c4a54/dqc_reference
[2024-01-24 13:49:19,053] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:19,054] [INFO] Task started: Prodigal
[2024-01-24 13:49:19,054] [INFO] Running command: gunzip -c /var/lib/cwl/stgcebb0c1b-8ccf-4f5f-b7b4-5d706996f8f0/GCF_000283015.1_P735.v1.0_genomic.fna.gz | prodigal -d GCF_000283015.1_P735.v1.0_genomic.fna/cds.fna -a GCF_000283015.1_P735.v1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:29,887] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:29,888] [INFO] Task started: HMMsearch
[2024-01-24 13:49:29,888] [INFO] Running command: hmmsearch --tblout GCF_000283015.1_P735.v1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg218bf336-dd62-4ee3-b2c7-2d03c61c4a54/dqc_reference/reference_markers.hmm GCF_000283015.1_P735.v1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:30,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:30,200] [INFO] Found 6/6 markers.
[2024-01-24 13:49:30,230] [INFO] Query marker FASTA was written to GCF_000283015.1_P735.v1.0_genomic.fna/markers.fasta
[2024-01-24 13:49:30,231] [INFO] Task started: Blastn
[2024-01-24 13:49:30,231] [INFO] Running command: blastn -query GCF_000283015.1_P735.v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg218bf336-dd62-4ee3-b2c7-2d03c61c4a54/dqc_reference/reference_markers.fasta -out GCF_000283015.1_P735.v1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:30,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:30,976] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:30,976] [INFO] Target genome list was writen to GCF_000283015.1_P735.v1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:49:30,984] [INFO] Task started: fastANI
[2024-01-24 13:49:30,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgcebb0c1b-8ccf-4f5f-b7b4-5d706996f8f0/GCF_000283015.1_P735.v1.0_genomic.fna.gz --refList GCF_000283015.1_P735.v1.0_genomic.fna/target_genomes.txt --output GCF_000283015.1_P735.v1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:44,020] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:44,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg218bf336-dd62-4ee3-b2c7-2d03c61c4a54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:44,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg218bf336-dd62-4ee3-b2c7-2d03c61c4a54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:44,041] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:44,041] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:44,041] [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
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	100.0	1106	1106	95	conclusive
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	99.9992	1105	1106	95	conclusive
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	80.4159	659	1106	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	79.7073	603	1106	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	79.6932	603	1106	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	79.6864	613	1106	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	79.6305	570	1106	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.6109	350	1106	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	78.5829	376	1106	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	78.5597	403	1106	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.449	437	1106	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.328	417	1106	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	78.3039	398	1106	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.2388	422	1106	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.8754	370	1106	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.5726	243	1106	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.4859	249	1106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:44,043] [INFO] DFAST Taxonomy check result was written to GCF_000283015.1_P735.v1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:49:44,044] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:44,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:44,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg218bf336-dd62-4ee3-b2c7-2d03c61c4a54/dqc_reference/checkm_data
[2024-01-24 13:49:44,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:44,085] [INFO] Task started: CheckM
[2024-01-24 13:49:44,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000283015.1_P735.v1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000283015.1_P735.v1.0_genomic.fna/checkm_input GCF_000283015.1_P735.v1.0_genomic.fna/checkm_result
[2024-01-24 13:50:21,785] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:21,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,803] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:21,803] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:21,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000283015.1_P735.v1.0_genomic.fna/markers.fasta)
[2024-01-24 13:50:21,804] [INFO] Task started: Blastn
[2024-01-24 13:50:21,805] [INFO] Running command: blastn -query GCF_000283015.1_P735.v1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg218bf336-dd62-4ee3-b2c7-2d03c61c4a54/dqc_reference/reference_markers_gtdb.fasta -out GCF_000283015.1_P735.v1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:22,832] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:22,835] [INFO] Selected 15 target genomes.
[2024-01-24 13:50:22,836] [INFO] Target genome list was writen to GCF_000283015.1_P735.v1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:22,845] [INFO] Task started: fastANI
[2024-01-24 13:50:22,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgcebb0c1b-8ccf-4f5f-b7b4-5d706996f8f0/GCF_000283015.1_P735.v1.0_genomic.fna.gz --refList GCF_000283015.1_P735.v1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000283015.1_P735.v1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:34,552] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:34,573] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:34,573] [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_900141715.1	s__Arenitalea lutea	99.9992	1105	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003143755.1	s__Algibacter_B sp003143755	80.425	658	1106	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_905480415.1	s__Algibacter_B sp905480415	79.6874	532	1106	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_014202225.1	s__Algibacter_B amylolyticus	79.6745	615	1106	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_900112595.1	s__Algibacter_B pectinivorans	79.6475	568	1106	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_900114265.1	s__Flaviramulus basaltis	79.4895	553	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	79.0673	497	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.8937	459	1106	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_001747085.1	s__Algibacter_C aquaticus	78.8419	442	1106	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_002741945.1	s__Wocania sp002741945	78.7896	451	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.6556	456	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642835.1	s__Tamlana_A agarivorans	78.5829	376	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCF_002893765.1	s__Tamlana_A carrageenivorans	78.5693	402	1106	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_008056315.1	s__Seonamhaeicola maritimus	78.4675	435	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	78.3053	399	1106	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:34,575] [INFO] GTDB search result was written to GCF_000283015.1_P735.v1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:34,576] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:34,580] [INFO] DFAST_QC result json was written to GCF_000283015.1_P735.v1.0_genomic.fna/dqc_result.json
[2024-01-24 13:50:34,581] [INFO] DFAST_QC completed!
[2024-01-24 13:50:34,581] [INFO] Total running time: 0h1m17s