[2024-01-24 13:37:05,083] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,090] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9922fcd-423b-4571-a3c5-c0d31f282b07/dqc_reference
[2024-01-24 13:37:06,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,529] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg3034f211-f4d3-46b2-8c55-6e107464850c/GCF_008017365.1_ASM801736v1_genomic.fna.gz | prodigal -d GCF_008017365.1_ASM801736v1_genomic.fna/cds.fna -a GCF_008017365.1_ASM801736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:33,965] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:33,966] [INFO] Task started: HMMsearch
[2024-01-24 13:37:33,966] [INFO] Running command: hmmsearch --tblout GCF_008017365.1_ASM801736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9922fcd-423b-4571-a3c5-c0d31f282b07/dqc_reference/reference_markers.hmm GCF_008017365.1_ASM801736v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:34,323] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:34,325] [INFO] Found 6/6 markers.
[2024-01-24 13:37:34,365] [INFO] Query marker FASTA was written to GCF_008017365.1_ASM801736v1_genomic.fna/markers.fasta
[2024-01-24 13:37:34,365] [INFO] Task started: Blastn
[2024-01-24 13:37:34,365] [INFO] Running command: blastn -query GCF_008017365.1_ASM801736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9922fcd-423b-4571-a3c5-c0d31f282b07/dqc_reference/reference_markers.fasta -out GCF_008017365.1_ASM801736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:35,050] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:35,054] [INFO] Selected 11 target genomes.
[2024-01-24 13:37:35,054] [INFO] Target genome list was writen to GCF_008017365.1_ASM801736v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:35,060] [INFO] Task started: fastANI
[2024-01-24 13:37:35,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg3034f211-f4d3-46b2-8c55-6e107464850c/GCF_008017365.1_ASM801736v1_genomic.fna.gz --refList GCF_008017365.1_ASM801736v1_genomic.fna/target_genomes.txt --output GCF_008017365.1_ASM801736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:45,773] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:45,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9922fcd-423b-4571-a3c5-c0d31f282b07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:45,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9922fcd-423b-4571-a3c5-c0d31f282b07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:45,788] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:45,788] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:45,788] [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
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	100.0	1417	1426	95	conclusive
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	100.0	1412	1426	95	conclusive
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	94.2338	1105	1426	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	94.22	1106	1426	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	87.7442	1091	1426	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	82.1043	710	1426	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	81.2569	680	1426	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	80.9999	666	1426	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	79.5642	559	1426	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.3557	207	1426	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	77.1579	83	1426	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:45,790] [INFO] DFAST Taxonomy check result was written to GCF_008017365.1_ASM801736v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:45,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:45,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:45,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9922fcd-423b-4571-a3c5-c0d31f282b07/dqc_reference/checkm_data
[2024-01-24 13:37:45,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:45,832] [INFO] Task started: CheckM
[2024-01-24 13:37:45,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008017365.1_ASM801736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008017365.1_ASM801736v1_genomic.fna/checkm_input GCF_008017365.1_ASM801736v1_genomic.fna/checkm_result
[2024-01-24 13:39:00,445] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:00,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:00,468] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:00,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:00,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008017365.1_ASM801736v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:00,470] [INFO] Task started: Blastn
[2024-01-24 13:39:00,470] [INFO] Running command: blastn -query GCF_008017365.1_ASM801736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9922fcd-423b-4571-a3c5-c0d31f282b07/dqc_reference/reference_markers_gtdb.fasta -out GCF_008017365.1_ASM801736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:01,299] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:01,303] [INFO] Selected 12 target genomes.
[2024-01-24 13:39:01,304] [INFO] Target genome list was writen to GCF_008017365.1_ASM801736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:01,326] [INFO] Task started: fastANI
[2024-01-24 13:39:01,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg3034f211-f4d3-46b2-8c55-6e107464850c/GCF_008017365.1_ASM801736v1_genomic.fna.gz --refList GCF_008017365.1_ASM801736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008017365.1_ASM801736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:11,427] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:11,438] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:11,438] [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_003584135.1	s__Muricauda sp003584135	100.0	1415	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_003584165.1	s__Muricauda sp003584165	94.2377	1105	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010500845.1	s__Muricauda sediminis	87.7358	1092	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	82.1043	710	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003584105.1	s__Muricauda taeanensis	81.2744	681	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_003058265.1	s__Muricauda sp003058265	80.994	667	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	80.1949	602	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_003992595.1	s__Muricauda sp002452975	80.0179	584	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	79.9674	679	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	79.4899	559	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385855.1	s__Muricauda sp003385855	79.3567	524	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_009184425.1	s__Muricauda olearia	79.105	531	1426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:11,440] [INFO] GTDB search result was written to GCF_008017365.1_ASM801736v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:11,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:11,445] [INFO] DFAST_QC result json was written to GCF_008017365.1_ASM801736v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:11,445] [INFO] DFAST_QC completed!
[2024-01-24 13:39:11,445] [INFO] Total running time: 0h2m6s