[2023-06-28 00:18:41,486] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:18:41,489] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:18:41,490] [INFO] DQC Reference Directory: /var/lib/cwl/stgea88fbd8-fd5c-4ca5-981a-427df983e451/dqc_reference
[2023-06-28 00:18:42,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:18:42,946] [INFO] Task started: Prodigal
[2023-06-28 00:18:42,946] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1f91736-549f-41f6-be6c-88105aaf5e44/GCA_026400985.1_ASM2640098v1_genomic.fna.gz | prodigal -d GCA_026400985.1_ASM2640098v1_genomic.fna/cds.fna -a GCA_026400985.1_ASM2640098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:18:52,447] [INFO] Task succeeded: Prodigal
[2023-06-28 00:18:52,448] [INFO] Task started: HMMsearch
[2023-06-28 00:18:52,448] [INFO] Running command: hmmsearch --tblout GCA_026400985.1_ASM2640098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea88fbd8-fd5c-4ca5-981a-427df983e451/dqc_reference/reference_markers.hmm GCA_026400985.1_ASM2640098v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:18:52,725] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:18:52,726] [INFO] Found 6/6 markers.
[2023-06-28 00:18:52,762] [INFO] Query marker FASTA was written to GCA_026400985.1_ASM2640098v1_genomic.fna/markers.fasta
[2023-06-28 00:18:52,762] [INFO] Task started: Blastn
[2023-06-28 00:18:52,762] [INFO] Running command: blastn -query GCA_026400985.1_ASM2640098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea88fbd8-fd5c-4ca5-981a-427df983e451/dqc_reference/reference_markers.fasta -out GCA_026400985.1_ASM2640098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:18:53,385] [INFO] Task succeeded: Blastn
[2023-06-28 00:18:53,389] [INFO] Selected 22 target genomes.
[2023-06-28 00:18:53,390] [INFO] Target genome list was writen to GCA_026400985.1_ASM2640098v1_genomic.fna/target_genomes.txt
[2023-06-28 00:18:53,403] [INFO] Task started: fastANI
[2023-06-28 00:18:53,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f91736-549f-41f6-be6c-88105aaf5e44/GCA_026400985.1_ASM2640098v1_genomic.fna.gz --refList GCA_026400985.1_ASM2640098v1_genomic.fna/target_genomes.txt --output GCA_026400985.1_ASM2640098v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:19:15,588] [INFO] Task succeeded: fastANI
[2023-06-28 00:19:15,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea88fbd8-fd5c-4ca5-981a-427df983e451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:19:15,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea88fbd8-fd5c-4ca5-981a-427df983e451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:19:15,590] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:19:15,590] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 00:19:15,590] [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
--------------------------------------------------------------------------------
[2023-06-28 00:19:15,592] [INFO] DFAST Taxonomy check result was written to GCA_026400985.1_ASM2640098v1_genomic.fna/tc_result.tsv
[2023-06-28 00:19:15,593] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:19:15,593] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:19:15,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea88fbd8-fd5c-4ca5-981a-427df983e451/dqc_reference/checkm_data
[2023-06-28 00:19:15,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:19:15,629] [INFO] Task started: CheckM
[2023-06-28 00:19:15,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400985.1_ASM2640098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400985.1_ASM2640098v1_genomic.fna/checkm_input GCA_026400985.1_ASM2640098v1_genomic.fna/checkm_result
[2023-06-28 00:19:46,439] [INFO] Task succeeded: CheckM
[2023-06-28 00:19:46,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:19:46,462] [INFO] ===== Completeness check finished =====
[2023-06-28 00:19:46,462] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:19:46,463] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400985.1_ASM2640098v1_genomic.fna/markers.fasta)
[2023-06-28 00:19:46,463] [INFO] Task started: Blastn
[2023-06-28 00:19:46,464] [INFO] Running command: blastn -query GCA_026400985.1_ASM2640098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea88fbd8-fd5c-4ca5-981a-427df983e451/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400985.1_ASM2640098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:19:47,214] [INFO] Task succeeded: Blastn
[2023-06-28 00:19:47,219] [INFO] Selected 19 target genomes.
[2023-06-28 00:19:47,219] [INFO] Target genome list was writen to GCA_026400985.1_ASM2640098v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:19:47,229] [INFO] Task started: fastANI
[2023-06-28 00:19:47,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1f91736-549f-41f6-be6c-88105aaf5e44/GCA_026400985.1_ASM2640098v1_genomic.fna.gz --refList GCA_026400985.1_ASM2640098v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400985.1_ASM2640098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:19:59,357] [INFO] Task succeeded: fastANI
[2023-06-28 00:19:59,373] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:19:59,374] [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
GCA_002737405.1	s__BAIKAL-G1-2R sp002737405	97.7496	806	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__BAIKAL-G1-2R	95.0	97.99	97.98	0.93	0.92	3	conclusive
GCA_903877395.1	s__BAIKAL-G1-2R sp903877395	78.6328	153	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__BAIKAL-G1-2R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670915.1	s__BAIKAL-G1-2R sp003670915	78.5953	106	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__BAIKAL-G1-2R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670865.1	s__BAIKAL-G1-2R sp003670865	76.9854	134	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__BAIKAL-G1-2R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885565.1	s__CAISJI01 sp903885565	76.6653	125	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__CAISJI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	76.5902	65	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	76.5421	67	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	76.3271	95	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670825.1	s__QWPN01 sp003670825	76.1856	64	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005791575.1	s__F1-20-MAGs016 sp005791575	75.9985	60	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	75.8801	81	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789975.1	s__QWPN01 sp005789975	75.8667	74	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.49	99.44	0.83	0.81	3	-
GCA_010027105.1	s__RGVT01 sp010027105	75.7225	66	885	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:19:59,376] [INFO] GTDB search result was written to GCA_026400985.1_ASM2640098v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:19:59,377] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:19:59,380] [INFO] DFAST_QC result json was written to GCA_026400985.1_ASM2640098v1_genomic.fna/dqc_result.json
[2023-06-28 00:19:59,380] [INFO] DFAST_QC completed!
[2023-06-28 00:19:59,380] [INFO] Total running time: 0h1m18s