[2024-01-24 12:29:37,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:37,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:37,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg70db1f0c-014d-44c0-8329-d25cf2155888/dqc_reference
[2024-01-24 12:29:39,267] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:39,268] [INFO] Task started: Prodigal
[2024-01-24 12:29:39,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg9138202f-7fe6-4c6b-94c0-71b0ca2ca4ec/GCF_021728675.1_ASM2172867v1_genomic.fna.gz | prodigal -d GCF_021728675.1_ASM2172867v1_genomic.fna/cds.fna -a GCF_021728675.1_ASM2172867v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:45,353] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:45,353] [INFO] Task started: HMMsearch
[2024-01-24 12:29:45,353] [INFO] Running command: hmmsearch --tblout GCF_021728675.1_ASM2172867v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70db1f0c-014d-44c0-8329-d25cf2155888/dqc_reference/reference_markers.hmm GCF_021728675.1_ASM2172867v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:45,599] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:45,601] [INFO] Found 6/6 markers.
[2024-01-24 12:29:45,629] [INFO] Query marker FASTA was written to GCF_021728675.1_ASM2172867v1_genomic.fna/markers.fasta
[2024-01-24 12:29:45,629] [INFO] Task started: Blastn
[2024-01-24 12:29:45,629] [INFO] Running command: blastn -query GCF_021728675.1_ASM2172867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70db1f0c-014d-44c0-8329-d25cf2155888/dqc_reference/reference_markers.fasta -out GCF_021728675.1_ASM2172867v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:46,415] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:46,420] [INFO] Selected 20 target genomes.
[2024-01-24 12:29:46,421] [INFO] Target genome list was writen to GCF_021728675.1_ASM2172867v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:46,432] [INFO] Task started: fastANI
[2024-01-24 12:29:46,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg9138202f-7fe6-4c6b-94c0-71b0ca2ca4ec/GCF_021728675.1_ASM2172867v1_genomic.fna.gz --refList GCF_021728675.1_ASM2172867v1_genomic.fna/target_genomes.txt --output GCF_021728675.1_ASM2172867v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:57,305] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:57,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70db1f0c-014d-44c0-8329-d25cf2155888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:57,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70db1f0c-014d-44c0-8329-d25cf2155888/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:57,327] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:29:57,327] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:29:57,327] [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
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	80.6987	343	650	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	80.6707	426	650	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	80.3806	383	650	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	80.3209	380	650	95	below_threshold
Neisseria animalis	strain=DSM 23392	GCA_003795365.1	492	492	type	True	80.2201	382	650	95	below_threshold
Neisseria sicca	strain=DSM 17713	GCA_014054945.1	490	490	suspected-type	True	79.9329	375	650	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	79.8633	355	650	95	below_threshold
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	79.8152	375	650	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	79.7803	373	650	95	below_threshold
Neisseria meningitidis	strain=NCTC10025	GCA_900638555.1	487	487	type	True	79.733	347	650	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	79.6984	347	650	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	79.6478	359	650	95	below_threshold
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	79.6343	355	650	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	79.5793	316	650	95	below_threshold
Neisseria iguanae	strain=ATCC 51483	GCA_003013245.1	90242	90242	type	True	79.4573	346	650	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	79.4552	343	650	95	below_threshold
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	79.3035	379	650	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	79.2718	384	650	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	79.2625	377	650	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.0108	326	650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:57,330] [INFO] DFAST Taxonomy check result was written to GCF_021728675.1_ASM2172867v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:57,330] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:57,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:57,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70db1f0c-014d-44c0-8329-d25cf2155888/dqc_reference/checkm_data
[2024-01-24 12:29:57,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:57,361] [INFO] Task started: CheckM
[2024-01-24 12:29:57,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021728675.1_ASM2172867v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021728675.1_ASM2172867v1_genomic.fna/checkm_input GCF_021728675.1_ASM2172867v1_genomic.fna/checkm_result
[2024-01-24 12:30:21,034] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:21,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:21,056] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:21,057] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:21,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021728675.1_ASM2172867v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:21,057] [INFO] Task started: Blastn
[2024-01-24 12:30:21,058] [INFO] Running command: blastn -query GCF_021728675.1_ASM2172867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70db1f0c-014d-44c0-8329-d25cf2155888/dqc_reference/reference_markers_gtdb.fasta -out GCF_021728675.1_ASM2172867v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:22,363] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:22,366] [INFO] Selected 24 target genomes.
[2024-01-24 12:30:22,366] [INFO] Target genome list was writen to GCF_021728675.1_ASM2172867v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:22,393] [INFO] Task started: fastANI
[2024-01-24 12:30:22,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg9138202f-7fe6-4c6b-94c0-71b0ca2ca4ec/GCF_021728675.1_ASM2172867v1_genomic.fna.gz --refList GCF_021728675.1_ASM2172867v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021728675.1_ASM2172867v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:34,848] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:34,871] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:30:34,871] [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_014898075.1	s__Neisseria sp011038745	82.432	403	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.25	98.87	0.98	0.97	4	-
GCF_001592185.1	s__Neisseria denitrificans	80.734	341	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900636515.1	s__Neisseria animalis	80.3712	377	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCA_001067655.1	s__Neisseria lactamica_B	80.0597	324	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_002216145.1	s__Neisseria chenwenguii	80.0115	404	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_014054945.1	s__Neisseria sicca	79.9546	371	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	99.97	99.97	1.00	1.00	2	-
GCF_001815675.1	s__Neisseria sp001815675	79.9021	371	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.4201	97.29	97.29	0.90	0.90	2	-
GCF_001809325.1	s__Neisseria sp001809325	79.8461	368	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_003044455.1	s__Neisseria bergeri	79.8042	338	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.18	96.14	0.94	0.92	5	-
GCF_003315235.1	s__Neisseria gonorrhoeae	79.7844	329	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	99.56	98.98	0.97	0.89	796	-
GCF_900638555.1	s__Neisseria meningitidis	79.7795	344	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	97.78	97.16	0.95	0.86	2138	-
GCF_013267835.1	s__Neisseria sp000186165	79.7465	374	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_000227275.1	s__Neisseria sp000227275	79.7433	390	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_000260655.1	s__Neisseria sicca_B	79.7016	365	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_003351665.1	s__Neisseria perflava	79.6767	354	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.77	96.48	0.96	0.95	5	-
GCF_005221285.1	s__Neisseria flavescens	79.6061	357	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.29	96.65	0.97	0.93	6	-
GCF_001618085.1	s__Neisseria flavescens_C	79.5389	351	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_003013245.1	s__Neisseria iguanae	79.477	343	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044645.1	s__Neisseria subflava_B	79.4109	362	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.654	N/A	N/A	N/A	N/A	1	-
GCF_014055005.1	s__Neisseria dentiae	79.2534	383	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_002108505.1	s__Neisseria dumasiana	79.1067	323	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_900187305.1	s__Neisseria zoodegmatis	78.9323	345	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_002237445.1	s__Neisseria sp002237445	78.6993	309	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_900636765.1	s__Neisseria canis	78.2813	242	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:34,874] [INFO] GTDB search result was written to GCF_021728675.1_ASM2172867v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:34,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:34,879] [INFO] DFAST_QC result json was written to GCF_021728675.1_ASM2172867v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:34,879] [INFO] DFAST_QC completed!
[2024-01-24 12:30:34,879] [INFO] Total running time: 0h0m57s