[2024-01-24 13:13:39,347] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,349] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,349] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf1bb551-f599-4c4a-ba67-78ab8226856e/dqc_reference
[2024-01-24 13:13:40,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,683] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,683] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2c84f37-fd8c-4df8-9150-bd34c1989c07/GCF_002770595.1_ASM277059v1_genomic.fna.gz | prodigal -d GCF_002770595.1_ASM277059v1_genomic.fna/cds.fna -a GCF_002770595.1_ASM277059v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:59,126] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:59,127] [INFO] Task started: HMMsearch
[2024-01-24 13:13:59,127] [INFO] Running command: hmmsearch --tblout GCF_002770595.1_ASM277059v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf1bb551-f599-4c4a-ba67-78ab8226856e/dqc_reference/reference_markers.hmm GCF_002770595.1_ASM277059v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:59,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:59,390] [INFO] Found 6/6 markers.
[2024-01-24 13:13:59,426] [INFO] Query marker FASTA was written to GCF_002770595.1_ASM277059v1_genomic.fna/markers.fasta
[2024-01-24 13:13:59,426] [INFO] Task started: Blastn
[2024-01-24 13:13:59,427] [INFO] Running command: blastn -query GCF_002770595.1_ASM277059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf1bb551-f599-4c4a-ba67-78ab8226856e/dqc_reference/reference_markers.fasta -out GCF_002770595.1_ASM277059v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:00,141] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:00,148] [INFO] Selected 27 target genomes.
[2024-01-24 13:14:00,148] [INFO] Target genome list was writen to GCF_002770595.1_ASM277059v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:00,166] [INFO] Task started: fastANI
[2024-01-24 13:14:00,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c84f37-fd8c-4df8-9150-bd34c1989c07/GCF_002770595.1_ASM277059v1_genomic.fna.gz --refList GCF_002770595.1_ASM277059v1_genomic.fna/target_genomes.txt --output GCF_002770595.1_ASM277059v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:21,767] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:21,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf1bb551-f599-4c4a-ba67-78ab8226856e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:21,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf1bb551-f599-4c4a-ba67-78ab8226856e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:21,787] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:21,787] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:21,788] [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
Chryseobacterium camelliae	strain=Dolsongi-HT1	GCA_002770595.1	1265445	1265445	type	True	100.0	1455	1458	95	conclusive
Chryseobacterium hagamense	strain=NBRC 105253	GCA_007991455.1	395935	395935	type	True	79.5456	644	1458	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	79.3276	518	1458	95	below_threshold
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	79.167	561	1458	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	79.1612	558	1458	95	below_threshold
Chryseobacterium phocaeense	strain=6021061333	GCA_900169075.1	1816690	1816690	type	True	79.0536	566	1458	95	below_threshold
Chryseobacterium gregarium	strain=DSM 19109	GCA_000430845.1	456299	456299	type	True	79.0393	594	1458	95	below_threshold
Chryseobacterium oranimense	strain=DSM 19055	GCA_900129755.1	421058	421058	type	True	78.9855	572	1458	95	below_threshold
Chryseobacterium taeanense	strain=DSM 17071	GCA_900099685.1	311334	311334	type	True	78.9516	488	1458	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	78.8927	390	1458	95	below_threshold
Chryseobacterium hispalense	strain=DSM 25574	GCA_000708615.2	1453492	1453492	type	True	78.8168	523	1458	95	below_threshold
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	78.7446	529	1458	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	78.7437	550	1458	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	78.6759	496	1458	95	below_threshold
Chryseobacterium candidae	strain=JC507	GCA_004916905.1	1978493	1978493	type	True	78.6518	507	1458	95	below_threshold
Chryseobacterium lathyri	strain=NBRC 105250	GCA_007991435.1	395933	395933	type	True	78.6119	507	1458	95	below_threshold
Chryseobacterium lathyri	strain=KCTC 22544	GCA_003290185.1	395933	395933	type	True	78.597	519	1458	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	78.577	468	1458	95	below_threshold
Chryseobacterium vrystaatense	strain=LMG 22846	GCA_000737765.1	307480	307480	type	True	78.5767	475	1458	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	78.5296	501	1458	95	below_threshold
Chryseobacterium culicis	strain=DSM 23031	GCA_900108365.1	680127	680127	type	True	78.5272	523	1458	95	below_threshold
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	78.499	503	1458	95	below_threshold
Chryseobacterium soli	strain=DSM 19298	GCA_000737705.1	445961	445961	type	True	78.4137	493	1458	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.4069	286	1458	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	78.0772	335	1458	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.5997	137	1458	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.5908	137	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:21,789] [INFO] DFAST Taxonomy check result was written to GCF_002770595.1_ASM277059v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:21,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:21,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:21,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf1bb551-f599-4c4a-ba67-78ab8226856e/dqc_reference/checkm_data
[2024-01-24 13:14:21,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:21,833] [INFO] Task started: CheckM
[2024-01-24 13:14:21,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002770595.1_ASM277059v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002770595.1_ASM277059v1_genomic.fna/checkm_input GCF_002770595.1_ASM277059v1_genomic.fna/checkm_result
[2024-01-24 13:15:14,576] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:14,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:14,595] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:14,596] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:14,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002770595.1_ASM277059v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:14,596] [INFO] Task started: Blastn
[2024-01-24 13:15:14,596] [INFO] Running command: blastn -query GCF_002770595.1_ASM277059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf1bb551-f599-4c4a-ba67-78ab8226856e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002770595.1_ASM277059v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:15,481] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:15,487] [INFO] Selected 25 target genomes.
[2024-01-24 13:15:15,487] [INFO] Target genome list was writen to GCF_002770595.1_ASM277059v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:15,513] [INFO] Task started: fastANI
[2024-01-24 13:15:15,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c84f37-fd8c-4df8-9150-bd34c1989c07/GCF_002770595.1_ASM277059v1_genomic.fna.gz --refList GCF_002770595.1_ASM277059v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002770595.1_ASM277059v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:35,973] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:35,992] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:35,993] [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_002770595.1	s__Chryseobacterium camelliae	100.0	1455	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008329705.1	s__Chryseobacterium sp008329705	79.9816	644	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603435.1	s__Chryseobacterium sp013153155	79.7625	582	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.28	96.28	0.93	0.93	2	-
GCF_007991455.1	s__Chryseobacterium hagamense	79.539	643	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002177115.1	s__Chryseobacterium mucoviscidosis	79.3096	520	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	-
GCF_001421435.1	s__Chryseobacterium sp001421435	79.2997	609	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156825.1	s__Chryseobacterium gambrini	79.1522	559	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_001295265.1	s__Chryseobacterium indologenes_A	79.0932	513	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430845.1	s__Chryseobacterium gregarium	79.0378	596	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129755.1	s__Chryseobacterium oranimense	79.0014	570	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.88	97.88	0.91	0.91	3	-
GCF_900099685.1	s__Chryseobacterium taeanense	78.9689	487	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384725.1	s__Chryseobacterium sp003384725	78.8414	478	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971235.1	s__Chryseobacterium aureum	78.7839	529	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156075.1	s__Chryseobacterium sp900156075	78.7595	380	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204415.1	s__Chryseobacterium defluvii_A	78.7482	472	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045445.1	s__Chryseobacterium sp001045445	78.7474	556	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737715.1	s__Chryseobacterium sp000737715	78.7322	533	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737785.1	s__Chryseobacterium luteum	78.7317	550	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115055.1	s__Chryseobacterium oleae	78.6759	496	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347605.1	s__Chryseobacterium sp003347605	78.6753	484	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916905.1	s__Chryseobacterium candidae	78.6678	505	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.64	98.56	0.91	0.91	3	-
GCF_002899945.2	s__Chryseobacterium viscerum	78.568	469	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.88	95.74	0.91	0.87	3	-
GCF_000737765.1	s__Chryseobacterium vrystaatense	78.5678	476	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.86	98.86	0.93	0.93	2	-
GCF_900128945.1	s__Chryseobacterium sp900128945	78.5616	513	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.14	97.03	0.94	0.94	3	-
GCF_001593385.1	s__Chryseobacterium cucumeris	78.507	502	1458	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.67	98.29	0.93	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:35,994] [INFO] GTDB search result was written to GCF_002770595.1_ASM277059v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:35,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:36,000] [INFO] DFAST_QC result json was written to GCF_002770595.1_ASM277059v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:36,000] [INFO] DFAST_QC completed!
[2024-01-24 13:15:36,000] [INFO] Total running time: 0h1m57s