[2024-01-24 10:57:50,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg45e7a41b-8740-4f16-bcb2-3fd70e1b96df/dqc_reference
[2024-01-24 10:57:52,640] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,641] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ed45a65-5d59-4464-9ec6-547319de2634/GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/cds.fna -a GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:18,883] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:18,883] [INFO] Task started: HMMsearch
[2024-01-24 10:58:18,883] [INFO] Running command: hmmsearch --tblout GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45e7a41b-8740-4f16-bcb2-3fd70e1b96df/dqc_reference/reference_markers.hmm GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:19,171] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:19,172] [INFO] Found 6/6 markers.
[2024-01-24 10:58:19,214] [INFO] Query marker FASTA was written to GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 10:58:19,214] [INFO] Task started: Blastn
[2024-01-24 10:58:19,214] [INFO] Running command: blastn -query GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg45e7a41b-8740-4f16-bcb2-3fd70e1b96df/dqc_reference/reference_markers.fasta -out GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:19,795] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:19,798] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:19,799] [INFO] Target genome list was writen to GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 10:58:19,805] [INFO] Task started: fastANI
[2024-01-24 10:58:19,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ed45a65-5d59-4464-9ec6-547319de2634/GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna.gz --refList GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:37,851] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:37,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45e7a41b-8740-4f16-bcb2-3fd70e1b96df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:37,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45e7a41b-8740-4f16-bcb2-3fd70e1b96df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:37,866] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:37,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:37,866] [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
Chitinophaga costaii	strain=A37T2	GCA_900094705.1	1335309	1335309	type	True	100.0	1661	1664	95	conclusive
Chitinophaga costaii	strain=A37T2	GCA_003071385.1	1335309	1335309	type	True	99.9996	1660	1664	95	conclusive
Chitinophaga parva	strain=LY-1	GCA_003071345.1	2169414	2169414	type	True	79.7985	821	1664	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	77.109	192	1664	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	77.0114	214	1664	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	76.9559	212	1664	95	below_threshold
Chitinophaga rupis	strain=DSM 21039	GCA_900109685.1	573321	573321	type	True	76.9479	271	1664	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	76.9289	200	1664	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	76.7614	236	1664	95	below_threshold
Chitinophaga solisilvae	strain=O9	GCA_009928525.1	1233460	1233460	type	True	76.7608	196	1664	95	below_threshold
Chitinophaga agrisoli	strain=BN140078	GCA_008386695.1	2607653	2607653	type	True	76.7496	231	1664	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	76.6394	213	1664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:37,868] [INFO] DFAST Taxonomy check result was written to GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 10:58:37,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:37,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:37,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45e7a41b-8740-4f16-bcb2-3fd70e1b96df/dqc_reference/checkm_data
[2024-01-24 10:58:37,870] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:37,917] [INFO] Task started: CheckM
[2024-01-24 10:58:37,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/checkm_input GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 10:59:47,367] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:47,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:47,388] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:47,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:47,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 10:59:47,389] [INFO] Task started: Blastn
[2024-01-24 10:59:47,389] [INFO] Running command: blastn -query GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg45e7a41b-8740-4f16-bcb2-3fd70e1b96df/dqc_reference/reference_markers_gtdb.fasta -out GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:48,217] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:48,222] [INFO] Selected 20 target genomes.
[2024-01-24 10:59:48,222] [INFO] Target genome list was writen to GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:48,275] [INFO] Task started: fastANI
[2024-01-24 10:59:48,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ed45a65-5d59-4464-9ec6-547319de2634/GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna.gz --refList GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:10,815] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:10,837] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:10,838] [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_900094705.1	s__Chitinophaga costaii	100.0	1661	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003071345.1	s__Chitinophaga parva	79.7919	822	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182155.1	s__Chitinophaga sp003182155	77.2203	142	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813775.1	s__Chitinophaga lutea	77.1219	191	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168175.1	s__Chitinophaga sp902168175	77.0906	158	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849435.1	s__Chitinophaga niabensis_A	77.0493	134	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641275.1	s__Chitinophaga varians_A	76.9685	219	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927205.1	s__Chitinophaga fulva	76.9559	211	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109685.1	s__Chitinophaga rupis	76.9471	270	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003308995.1	s__Chitinophaga flava	76.9418	199	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641265.1	s__Chitinophaga eiseniae_A	76.931	208	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829335.1	s__Chitinophaga polysaccharea_B	76.9228	211	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091455.1	s__Chitinophaga sp019091455	76.8983	276	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112615.1	s__Chitinophaga sp900112615	76.8942	154	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003994345.2	s__Chitinophaga extrema	76.8096	196	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.60	98.60	0.96	0.96	2	-
GCF_008386695.1	s__Chitinophaga agrisoli	76.7596	230	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017742215.1	s__Chitinophaga sp017742215	76.6497	212	1664	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:10,840] [INFO] GTDB search result was written to GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:10,841] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:10,846] [INFO] DFAST_QC result json was written to GCF_900094705.1_IMG-taxon_2671180112_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:00:10,846] [INFO] DFAST_QC completed!
[2024-01-24 11:00:10,846] [INFO] Total running time: 0h2m21s