[2024-01-24 12:39:47,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:47,948] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:47,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgaae0a98e-9a4c-4eef-b183-0ceb1fadeb9c/dqc_reference
[2024-01-24 12:39:49,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:49,091] [INFO] Task started: Prodigal
[2024-01-24 12:39:49,091] [INFO] Running command: gunzip -c /var/lib/cwl/stg50ea4e5f-76e6-40b8-9a97-253d3ca41573/GCF_021278965.1_ASM2127896v1_genomic.fna.gz | prodigal -d GCF_021278965.1_ASM2127896v1_genomic.fna/cds.fna -a GCF_021278965.1_ASM2127896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:07,914] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:07,915] [INFO] Task started: HMMsearch
[2024-01-24 12:40:07,915] [INFO] Running command: hmmsearch --tblout GCF_021278965.1_ASM2127896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaae0a98e-9a4c-4eef-b183-0ceb1fadeb9c/dqc_reference/reference_markers.hmm GCF_021278965.1_ASM2127896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:08,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:08,198] [INFO] Found 6/6 markers.
[2024-01-24 12:40:08,240] [INFO] Query marker FASTA was written to GCF_021278965.1_ASM2127896v1_genomic.fna/markers.fasta
[2024-01-24 12:40:08,240] [INFO] Task started: Blastn
[2024-01-24 12:40:08,240] [INFO] Running command: blastn -query GCF_021278965.1_ASM2127896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae0a98e-9a4c-4eef-b183-0ceb1fadeb9c/dqc_reference/reference_markers.fasta -out GCF_021278965.1_ASM2127896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:08,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:08,933] [INFO] Selected 10 target genomes.
[2024-01-24 12:40:08,934] [INFO] Target genome list was writen to GCF_021278965.1_ASM2127896v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:08,937] [INFO] Task started: fastANI
[2024-01-24 12:40:08,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ea4e5f-76e6-40b8-9a97-253d3ca41573/GCF_021278965.1_ASM2127896v1_genomic.fna.gz --refList GCF_021278965.1_ASM2127896v1_genomic.fna/target_genomes.txt --output GCF_021278965.1_ASM2127896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:20,260] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:20,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaae0a98e-9a4c-4eef-b183-0ceb1fadeb9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:20,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaae0a98e-9a4c-4eef-b183-0ceb1fadeb9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:20,270] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:20,271] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:20,271] [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 nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	87.7467	1403	1785	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	87.4393	1167	1785	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	87.3862	1422	1785	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	87.3017	1304	1785	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	86.9019	1366	1785	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	84.688	1193	1785	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	84.4583	1161	1785	95	below_threshold
Chryseobacterium arthrosphaerae	strain=CC-VM-7	GCA_001684965.1	651561	651561	type	True	83.0654	1122	1785	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.2801	739	1785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:20,273] [INFO] DFAST Taxonomy check result was written to GCF_021278965.1_ASM2127896v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:20,274] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:20,274] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:20,274] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaae0a98e-9a4c-4eef-b183-0ceb1fadeb9c/dqc_reference/checkm_data
[2024-01-24 12:40:20,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:20,336] [INFO] Task started: CheckM
[2024-01-24 12:40:20,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021278965.1_ASM2127896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021278965.1_ASM2127896v1_genomic.fna/checkm_input GCF_021278965.1_ASM2127896v1_genomic.fna/checkm_result
[2024-01-24 12:41:16,937] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:16,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:16,953] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:16,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:16,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021278965.1_ASM2127896v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:16,954] [INFO] Task started: Blastn
[2024-01-24 12:41:16,954] [INFO] Running command: blastn -query GCF_021278965.1_ASM2127896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae0a98e-9a4c-4eef-b183-0ceb1fadeb9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_021278965.1_ASM2127896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:17,930] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:17,934] [INFO] Selected 14 target genomes.
[2024-01-24 12:41:17,934] [INFO] Target genome list was writen to GCF_021278965.1_ASM2127896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:17,942] [INFO] Task started: fastANI
[2024-01-24 12:41:17,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ea4e5f-76e6-40b8-9a97-253d3ca41573/GCF_021278965.1_ASM2127896v1_genomic.fna.gz --refList GCF_021278965.1_ASM2127896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021278965.1_ASM2127896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:34,610] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:34,621] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:34,621] [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_900078205.2	s__Chryseobacterium timonianum	99.9678	1763	1785	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_003815715.1	s__Chryseobacterium sp003815715	87.8861	1395	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637665.1	s__Chryseobacterium nakagawai	87.7478	1403	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	87.4563	1367	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684955.1	s__Chryseobacterium contaminans	87.4473	1167	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004119455.1	s__Chryseobacterium sp004119455	87.3994	1363	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900100075.1	s__Chryseobacterium jejuense	87.3849	1422	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000829375.1	s__Chryseobacterium sp000829375	87.3259	1385	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385515.1	s__Chryseobacterium sp003385515	86.8988	1367	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.92	97.92	0.86	0.86	2	-
GCF_009900745.1	s__Chryseobacterium sp009900745	86.6267	1356	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	86.5212	1294	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
GCF_001684975.1	s__Chryseobacterium artocarpi	84.4668	1159	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835665.1	s__Chryseobacterium sp002835665	83.6051	887	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236175.1	s__Chryseobacterium sp019236175	82.6919	1033	1785	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:34,623] [INFO] GTDB search result was written to GCF_021278965.1_ASM2127896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:34,623] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:34,626] [INFO] DFAST_QC result json was written to GCF_021278965.1_ASM2127896v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:34,627] [INFO] DFAST_QC completed!
[2024-01-24 12:41:34,627] [INFO] Total running time: 0h1m47s