[2023-06-29 19:14:26,650] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:14:26,653] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:14:26,653] [INFO] DQC Reference Directory: /var/lib/cwl/stge552cafe-2a13-470e-9cff-79dd105682a1/dqc_reference
[2023-06-29 19:14:28,103] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:14:28,104] [INFO] Task started: Prodigal
[2023-06-29 19:14:28,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg851b586c-5004-4a54-8cbe-e539edfe6f76/GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna.gz | prodigal -d GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/cds.fna -a GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:14:37,107] [INFO] Task succeeded: Prodigal
[2023-06-29 19:14:37,107] [INFO] Task started: HMMsearch
[2023-06-29 19:14:37,107] [INFO] Running command: hmmsearch --tblout GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge552cafe-2a13-470e-9cff-79dd105682a1/dqc_reference/reference_markers.hmm GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:14:37,420] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:14:37,422] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg851b586c-5004-4a54-8cbe-e539edfe6f76/GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna.gz]
[2023-06-29 19:14:37,468] [INFO] Query marker FASTA was written to GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/markers.fasta
[2023-06-29 19:14:37,469] [INFO] Task started: Blastn
[2023-06-29 19:14:37,469] [INFO] Running command: blastn -query GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/markers.fasta -db /var/lib/cwl/stge552cafe-2a13-470e-9cff-79dd105682a1/dqc_reference/reference_markers.fasta -out GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:38,188] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:38,193] [INFO] Selected 29 target genomes.
[2023-06-29 19:14:38,193] [INFO] Target genome list was writen to GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/target_genomes.txt
[2023-06-29 19:14:38,195] [INFO] Task started: fastANI
[2023-06-29 19:14:38,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg851b586c-5004-4a54-8cbe-e539edfe6f76/GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna.gz --refList GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/target_genomes.txt --output GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:14:59,296] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:59,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge552cafe-2a13-470e-9cff-79dd105682a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:14:59,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge552cafe-2a13-470e-9cff-79dd105682a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:14:59,301] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:14:59,301] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:14:59,301] [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
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	74.7635	54	1044	95	below_threshold
Tepidimonas sediminis	strain=YIM 72259	GCA_007556605.1	2588941	2588941	type	True	74.7057	51	1044	95	below_threshold
Kitasatospora griseola	strain=JCM 3339	GCA_014648555.1	2064	2064	type	True	74.6136	57	1044	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:14:59,303] [INFO] DFAST Taxonomy check result was written to GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/tc_result.tsv
[2023-06-29 19:14:59,304] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:14:59,304] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:14:59,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge552cafe-2a13-470e-9cff-79dd105682a1/dqc_reference/checkm_data
[2023-06-29 19:14:59,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:14:59,344] [INFO] Task started: CheckM
[2023-06-29 19:14:59,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/checkm_input GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/checkm_result
[2023-06-29 19:15:30,407] [INFO] Task succeeded: CheckM
[2023-06-29 19:15:30,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:15:30,433] [INFO] ===== Completeness check finished =====
[2023-06-29 19:15:30,434] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:15:30,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/markers.fasta)
[2023-06-29 19:15:30,435] [INFO] Task started: Blastn
[2023-06-29 19:15:30,435] [INFO] Running command: blastn -query GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/markers.fasta -db /var/lib/cwl/stge552cafe-2a13-470e-9cff-79dd105682a1/dqc_reference/reference_markers_gtdb.fasta -out GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:15:31,417] [INFO] Task succeeded: Blastn
[2023-06-29 19:15:31,422] [INFO] Selected 26 target genomes.
[2023-06-29 19:15:31,423] [INFO] Target genome list was writen to GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:15:31,449] [INFO] Task started: fastANI
[2023-06-29 19:15:31,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg851b586c-5004-4a54-8cbe-e539edfe6f76/GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna.gz --refList GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/target_genomes_gtdb.txt --output GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:15:48,348] [INFO] Task succeeded: fastANI
[2023-06-29 19:15:48,367] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:15:48,368] [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_002794705.1	s__CP2-2F sp002794705	82.2676	482	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__UBA2796;g__CP2-2F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017743585.1	s__CP2-2F sp017743585	80.4363	535	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__UBA2796;g__CP2-2F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695215.1	s__CP2-2F sp003695215	80.2194	643	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__UBA2796;g__CP2-2F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879835.1	s__UBA2796 sp014879835	76.0444	50	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__UBA2796;g__UBA2796	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716525.1	s__OLB13 sp016716525	75.7626	65	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002332795.1	s__UBA2029 sp002332795	75.6905	82	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__UBA2029	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075625.1	s__UBA2796 sp002352035	75.689	76	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__UBA2796;g__UBA2796	95.0	99.81	99.81	0.99	0.99	2	-
GCA_012729765.1	s__JAAYCM01 sp012729765	75.6743	110	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__JAAYCM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789005.1	s__OLB15 sp016789005	75.647	136	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016927535.1	s__JAFGMM01 sp016927535	75.6073	87	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__JAFGMM01;g__JAFGMM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367385.1	s__SpSt-583 sp011367385	75.5161	83	1044	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_018432315.1	s__LM3-B42 sp018432315	75.4906	131	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__LM3-B42	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717205.1	s__OLB15 sp016717205	75.4798	95	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	97.47	97.38	0.90	0.87	3	-
GCA_014338005.1	s__CFX2 sp014338005	75.4792	66	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	98.19	98.19	0.87	0.87	2	-
GCA_013178165.1	s__Ch27 sp013178165	75.4285	62	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Ch27;g__Ch27	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010092855.1	s__TC-15 sp010092855	75.3185	53	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__TC-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788625.1	s__CFX2 sp016788625	75.3035	88	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388745.1	s__JACAER01 sp013388745	75.0991	86	1044	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__JACAER01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:15:48,370] [INFO] GTDB search result was written to GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:15:48,371] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:15:48,374] [INFO] DFAST_QC result json was written to GCA_937944335.1_N1_Bin_METABAT_251_1_genomic.fna/dqc_result.json
[2023-06-29 19:15:48,374] [INFO] DFAST_QC completed!
[2023-06-29 19:15:48,374] [INFO] Total running time: 0h1m22s