[2024-01-24 13:22:55,373] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,375] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c7c611e-4160-4eca-bfe5-c4f970c67954/dqc_reference
[2024-01-24 13:22:56,738] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,738] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg41d0ace3-fcbd-46fe-8b9b-1cf2e4976bb4/GCF_001050255.2_ASM105025v2_genomic.fna.gz | prodigal -d GCF_001050255.2_ASM105025v2_genomic.fna/cds.fna -a GCF_001050255.2_ASM105025v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:10,140] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:10,141] [INFO] Task started: HMMsearch
[2024-01-24 13:23:10,141] [INFO] Running command: hmmsearch --tblout GCF_001050255.2_ASM105025v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c7c611e-4160-4eca-bfe5-c4f970c67954/dqc_reference/reference_markers.hmm GCF_001050255.2_ASM105025v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:10,511] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:10,513] [INFO] Found 6/6 markers.
[2024-01-24 13:23:10,554] [INFO] Query marker FASTA was written to GCF_001050255.2_ASM105025v2_genomic.fna/markers.fasta
[2024-01-24 13:23:10,554] [INFO] Task started: Blastn
[2024-01-24 13:23:10,554] [INFO] Running command: blastn -query GCF_001050255.2_ASM105025v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c7c611e-4160-4eca-bfe5-c4f970c67954/dqc_reference/reference_markers.fasta -out GCF_001050255.2_ASM105025v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:11,177] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:11,180] [INFO] Selected 17 target genomes.
[2024-01-24 13:23:11,180] [INFO] Target genome list was writen to GCF_001050255.2_ASM105025v2_genomic.fna/target_genomes.txt
[2024-01-24 13:23:11,208] [INFO] Task started: fastANI
[2024-01-24 13:23:11,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg41d0ace3-fcbd-46fe-8b9b-1cf2e4976bb4/GCF_001050255.2_ASM105025v2_genomic.fna.gz --refList GCF_001050255.2_ASM105025v2_genomic.fna/target_genomes.txt --output GCF_001050255.2_ASM105025v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:23,084] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:23,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c7c611e-4160-4eca-bfe5-c4f970c67954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:23,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c7c611e-4160-4eca-bfe5-c4f970c67954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:23,092] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:23:23,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:23,092] [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
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	99.9995	1367	1381	95	conclusive
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	99.8712	1310	1381	95	conclusive
Ornatilinea apprima	strain=P3M-1	GCA_001306115.1	1134406	1134406	type	True	77.0976	140	1381	95	below_threshold
Longilinea arvoryzae	strain=KOME-1	GCA_001050235.2	360412	360412	type	True	77.0314	144	1381	95	below_threshold
Anaerolinea thermophila	strain=UNI-1	GCA_000199675.1	167964	167964	type	True	76.2013	92	1381	95	below_threshold
Anaerolinea thermolimosa	strain=IMO-1	GCA_001050195.2	229919	229919	type	True	75.9277	71	1381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:23,094] [INFO] DFAST Taxonomy check result was written to GCF_001050255.2_ASM105025v2_genomic.fna/tc_result.tsv
[2024-01-24 13:23:23,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:23,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:23,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c7c611e-4160-4eca-bfe5-c4f970c67954/dqc_reference/checkm_data
[2024-01-24 13:23:23,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:23,140] [INFO] Task started: CheckM
[2024-01-24 13:23:23,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050255.2_ASM105025v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050255.2_ASM105025v2_genomic.fna/checkm_input GCF_001050255.2_ASM105025v2_genomic.fna/checkm_result
[2024-01-24 13:24:03,876] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:03,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:03,905] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:03,905] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:03,905] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050255.2_ASM105025v2_genomic.fna/markers.fasta)
[2024-01-24 13:24:03,906] [INFO] Task started: Blastn
[2024-01-24 13:24:03,906] [INFO] Running command: blastn -query GCF_001050255.2_ASM105025v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c7c611e-4160-4eca-bfe5-c4f970c67954/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050255.2_ASM105025v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:04,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:04,785] [INFO] Selected 21 target genomes.
[2024-01-24 13:24:04,786] [INFO] Target genome list was writen to GCF_001050255.2_ASM105025v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:04,817] [INFO] Task started: fastANI
[2024-01-24 13:24:04,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg41d0ace3-fcbd-46fe-8b9b-1cf2e4976bb4/GCF_001050255.2_ASM105025v2_genomic.fna.gz --refList GCF_001050255.2_ASM105025v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001050255.2_ASM105025v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:18,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:18,330] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:18,330] [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_001306035.1	s__Levilinea saccharolytica	99.8746	1309	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Levilinea	95.0	99.90	99.90	0.95	0.95	2	conclusive
GCF_001306115.1	s__Ornatilinea apprima	77.0292	138	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Ornatilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050235.1	s__Longilinea arvoryzae	77.0067	145	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Longilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385985.1	s__UBA3924 sp002385985	76.7853	151	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA3924	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002298885.1	s__UBA700 sp002298885	76.2314	113	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA700	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000199675.1	s__Anaerolinea thermophila	76.2198	91	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011322445.1	s__DRMV01 sp011322445	76.1786	64	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__DRMV01;g__DRMV01	95.0	98.57	98.55	0.95	0.95	3	-
GCA_016927865.1	s__Anaerolinea sp016927865	76.139	155	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050195.2	s__Anaerolinea thermolimosa	76.1308	72	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Anaerolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002412925.1	s__UBA5195 sp002412925	76.1259	76	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5195	95.0	99.92	99.92	0.94	0.94	2	-
GCA_011367365.1	s__DSYU01 sp011367365	76.0823	150	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__DSYU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798515.1	s__JAAZNB01 sp012798515	75.943	138	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__JAAZNB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051635.1	s__DRKV01 sp011051635	75.9399	65	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__DRKV01;g__DRKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011176535.1	s__DUEP01 sp011176535	75.8425	58	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__DRMV01;g__DUEP01	95.0	99.79	99.71	0.93	0.89	3	-
GCA_016789165.1	s__SpSt-583 sp016789165	75.5356	85	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213135.1	s__JACRBQ01 sp016213135	75.2396	78	1381	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__VGOW01;g__JACRBQ01	95.0	98.48	98.48	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:18,332] [INFO] GTDB search result was written to GCF_001050255.2_ASM105025v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:18,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:18,336] [INFO] DFAST_QC result json was written to GCF_001050255.2_ASM105025v2_genomic.fna/dqc_result.json
[2024-01-24 13:24:18,336] [INFO] DFAST_QC completed!
[2024-01-24 13:24:18,336] [INFO] Total running time: 0h1m23s