[2024-01-25 18:40:50,879] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:50,880] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:50,881] [INFO] DQC Reference Directory: /var/lib/cwl/stg825be603-1685-4b77-9a47-06e3eb2cb122/dqc_reference
[2024-01-25 18:40:52,132] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:52,133] [INFO] Task started: Prodigal
[2024-01-25 18:40:52,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b7aa5f2-9c31-45c8-8208-411345a058ba/GCF_003071385.1_ASM307138v1_genomic.fna.gz | prodigal -d GCF_003071385.1_ASM307138v1_genomic.fna/cds.fna -a GCF_003071385.1_ASM307138v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:14,726] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:14,726] [INFO] Task started: HMMsearch
[2024-01-25 18:41:14,726] [INFO] Running command: hmmsearch --tblout GCF_003071385.1_ASM307138v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg825be603-1685-4b77-9a47-06e3eb2cb122/dqc_reference/reference_markers.hmm GCF_003071385.1_ASM307138v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:15,057] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:15,061] [INFO] Found 6/6 markers.
[2024-01-25 18:41:15,115] [INFO] Query marker FASTA was written to GCF_003071385.1_ASM307138v1_genomic.fna/markers.fasta
[2024-01-25 18:41:15,115] [INFO] Task started: Blastn
[2024-01-25 18:41:15,115] [INFO] Running command: blastn -query GCF_003071385.1_ASM307138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg825be603-1685-4b77-9a47-06e3eb2cb122/dqc_reference/reference_markers.fasta -out GCF_003071385.1_ASM307138v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:15,675] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:15,678] [INFO] Selected 17 target genomes.
[2024-01-25 18:41:15,678] [INFO] Target genome list was writen to GCF_003071385.1_ASM307138v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:15,684] [INFO] Task started: fastANI
[2024-01-25 18:41:15,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b7aa5f2-9c31-45c8-8208-411345a058ba/GCF_003071385.1_ASM307138v1_genomic.fna.gz --refList GCF_003071385.1_ASM307138v1_genomic.fna/target_genomes.txt --output GCF_003071385.1_ASM307138v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:34,909] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:34,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg825be603-1685-4b77-9a47-06e3eb2cb122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:34,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg825be603-1685-4b77-9a47-06e3eb2cb122/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:34,919] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:41:34,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:34,919] [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_003071385.1	1335309	1335309	type	True	100.0	1676	1677	95	conclusive
Chitinophaga costaii	strain=A37T2	GCA_900094705.1	1335309	1335309	type	True	99.9851	1655	1677	95	conclusive
Chitinophaga parva	strain=LY-1	GCA_003071345.1	2169414	2169414	type	True	79.9117	799	1677	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	77.1881	182	1677	95	below_threshold
Chitinophaga flava	strain=GDMCC 1.1325	GCA_003308995.1	2259036	2259036	type	True	77.1246	192	1677	95	below_threshold
Chitinophaga rupis	strain=DSM 21039	GCA_900109685.1	573321	573321	type	True	77.0044	266	1677	95	below_threshold
Chitinophaga solisilvae	strain=O9	GCA_009928525.1	1233460	1233460	type	True	76.9285	185	1677	95	below_threshold
Chitinophaga oryzae	strain=1303	GCA_012516375.2	2725414	2725414	type	True	76.8989	243	1677	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	76.8509	226	1677	95	below_threshold
Chitinophaga fulva	strain=G-6-1-13	GCA_012927205.1	2728842	2728842	type	True	76.8495	215	1677	95	below_threshold
Chitinophaga chungangae	strain=MAH-28	GCA_017742215.1	2821488	2821488	type	True	76.7724	194	1677	95	below_threshold
Chitinophaga agrisoli	strain=BN140078	GCA_008386695.1	2607653	2607653	type	True	76.6982	236	1677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:34,921] [INFO] DFAST Taxonomy check result was written to GCF_003071385.1_ASM307138v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:34,922] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:34,922] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:34,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg825be603-1685-4b77-9a47-06e3eb2cb122/dqc_reference/checkm_data
[2024-01-25 18:41:34,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:34,976] [INFO] Task started: CheckM
[2024-01-25 18:41:34,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003071385.1_ASM307138v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003071385.1_ASM307138v1_genomic.fna/checkm_input GCF_003071385.1_ASM307138v1_genomic.fna/checkm_result
[2024-01-25 18:42:34,313] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:34,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:34,333] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:34,334] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:34,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003071385.1_ASM307138v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:34,335] [INFO] Task started: Blastn
[2024-01-25 18:42:34,336] [INFO] Running command: blastn -query GCF_003071385.1_ASM307138v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg825be603-1685-4b77-9a47-06e3eb2cb122/dqc_reference/reference_markers_gtdb.fasta -out GCF_003071385.1_ASM307138v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:35,140] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:35,143] [INFO] Selected 20 target genomes.
[2024-01-25 18:42:35,143] [INFO] Target genome list was writen to GCF_003071385.1_ASM307138v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:35,173] [INFO] Task started: fastANI
[2024-01-25 18:42:35,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b7aa5f2-9c31-45c8-8208-411345a058ba/GCF_003071385.1_ASM307138v1_genomic.fna.gz --refList GCF_003071385.1_ASM307138v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003071385.1_ASM307138v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:58,880] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:58,890] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:58,891] [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	99.9851	1655	1677	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	79.9185	798	1677	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	77.2272	211	1677	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	77.2025	181	1677	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	77.1536	190	1677	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	77.0665	136	1677	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	77.0033	266	1677	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	76.994	192	1677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	98.60	98.60	0.96	0.96	2	-
GCF_019091455.1	s__Chitinophaga sp019091455	76.9421	282	1677	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	76.8967	171	1677	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	76.8376	215	1677	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	76.7847	160	1677	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	76.7724	194	1677	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	76.7523	221	1677	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	76.7155	158	1677	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	76.7114	227	1677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386695.1	s__Chitinophaga agrisoli	76.6982	236	1677	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:58,892] [INFO] GTDB search result was written to GCF_003071385.1_ASM307138v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:58,893] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:58,897] [INFO] DFAST_QC result json was written to GCF_003071385.1_ASM307138v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:58,897] [INFO] DFAST_QC completed!
[2024-01-25 18:42:58,897] [INFO] Total running time: 0h2m8s