[2023-06-19 10:06:02,210] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:06:02,213] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:06:02,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgd57451b9-7ff2-4d95-8fe6-88bcc7f32c5a/dqc_reference
[2023-06-19 10:06:03,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:06:03,402] [INFO] Task started: Prodigal
[2023-06-19 10:06:03,402] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb1293af-f7c6-465e-abc6-8d2bcd233f62/GCA_013697965.1_ASM1369796v1_genomic.fna.gz | prodigal -d GCA_013697965.1_ASM1369796v1_genomic.fna/cds.fna -a GCA_013697965.1_ASM1369796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:06:07,722] [INFO] Task succeeded: Prodigal
[2023-06-19 10:06:07,723] [INFO] Task started: HMMsearch
[2023-06-19 10:06:07,723] [INFO] Running command: hmmsearch --tblout GCA_013697965.1_ASM1369796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd57451b9-7ff2-4d95-8fe6-88bcc7f32c5a/dqc_reference/reference_markers.hmm GCA_013697965.1_ASM1369796v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:06:07,931] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:06:07,933] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb1293af-f7c6-465e-abc6-8d2bcd233f62/GCA_013697965.1_ASM1369796v1_genomic.fna.gz]
[2023-06-19 10:06:07,968] [INFO] Query marker FASTA was written to GCA_013697965.1_ASM1369796v1_genomic.fna/markers.fasta
[2023-06-19 10:06:07,968] [INFO] Task started: Blastn
[2023-06-19 10:06:07,968] [INFO] Running command: blastn -query GCA_013697965.1_ASM1369796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd57451b9-7ff2-4d95-8fe6-88bcc7f32c5a/dqc_reference/reference_markers.fasta -out GCA_013697965.1_ASM1369796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:06:08,606] [INFO] Task succeeded: Blastn
[2023-06-19 10:06:08,612] [INFO] Selected 25 target genomes.
[2023-06-19 10:06:08,612] [INFO] Target genome list was writen to GCA_013697965.1_ASM1369796v1_genomic.fna/target_genomes.txt
[2023-06-19 10:06:08,615] [INFO] Task started: fastANI
[2023-06-19 10:06:08,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1293af-f7c6-465e-abc6-8d2bcd233f62/GCA_013697965.1_ASM1369796v1_genomic.fna.gz --refList GCA_013697965.1_ASM1369796v1_genomic.fna/target_genomes.txt --output GCA_013697965.1_ASM1369796v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:06:23,880] [INFO] Task succeeded: fastANI
[2023-06-19 10:06:23,881] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd57451b9-7ff2-4d95-8fe6-88bcc7f32c5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:06:23,881] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd57451b9-7ff2-4d95-8fe6-88bcc7f32c5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:06:23,889] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:06:23,889] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 10:06:23,889] [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
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.8198	56	445	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.7735	55	445	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:06:23,892] [INFO] DFAST Taxonomy check result was written to GCA_013697965.1_ASM1369796v1_genomic.fna/tc_result.tsv
[2023-06-19 10:06:23,892] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:06:23,892] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:06:23,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd57451b9-7ff2-4d95-8fe6-88bcc7f32c5a/dqc_reference/checkm_data
[2023-06-19 10:06:23,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:06:23,920] [INFO] Task started: CheckM
[2023-06-19 10:06:23,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013697965.1_ASM1369796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013697965.1_ASM1369796v1_genomic.fna/checkm_input GCA_013697965.1_ASM1369796v1_genomic.fna/checkm_result
[2023-06-19 10:06:43,397] [INFO] Task succeeded: CheckM
[2023-06-19 10:06:43,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:06:43,423] [INFO] ===== Completeness check finished =====
[2023-06-19 10:06:43,423] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:06:43,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013697965.1_ASM1369796v1_genomic.fna/markers.fasta)
[2023-06-19 10:06:43,424] [INFO] Task started: Blastn
[2023-06-19 10:06:43,424] [INFO] Running command: blastn -query GCA_013697965.1_ASM1369796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd57451b9-7ff2-4d95-8fe6-88bcc7f32c5a/dqc_reference/reference_markers_gtdb.fasta -out GCA_013697965.1_ASM1369796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:06:44,422] [INFO] Task succeeded: Blastn
[2023-06-19 10:06:44,427] [INFO] Selected 19 target genomes.
[2023-06-19 10:06:44,428] [INFO] Target genome list was writen to GCA_013697965.1_ASM1369796v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:06:44,436] [INFO] Task started: fastANI
[2023-06-19 10:06:44,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1293af-f7c6-465e-abc6-8d2bcd233f62/GCA_013697965.1_ASM1369796v1_genomic.fna.gz --refList GCA_013697965.1_ASM1369796v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013697965.1_ASM1369796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:06:52,609] [INFO] Task succeeded: fastANI
[2023-06-19 10:06:52,627] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 10:06:52,627] [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_013698385.1	s__SPCO01 sp013698385	79.6524	183	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__SPCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200745.1	s__SPCO01 sp016200745	78.6768	154	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__SPCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698095.1	s__CF-46 sp013698095	78.6303	189	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250155.1	s__UBA5189 sp003250155	78.5562	104	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	99.47	99.47	0.88	0.88	2	-
GCA_013695255.1	s__JACDAV01 sp013695255	78.504	133	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__JACDAV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297395.1	s__UBA5189 sp004297395	78.4366	155	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005889475.1	s__UBA5189 sp005889475	78.3686	135	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298915.1	s__UBA5189 sp004298915	78.3132	96	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881915.1	s__Palsa-1033 sp017881915	78.2952	143	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003169655.1	s__Palsa-1033 sp003169655	78.1942	155	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191345.1	s__UBA5189 sp016191345	78.1798	153	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001795245.1	s__UBA5189 sp001795245	78.0858	153	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200665.1	s__UBA5189 sp016200665	77.9845	135	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200675.1	s__UBA5189 sp016200675	77.8337	136	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881055.1	s__C-114 sp005881055	77.8176	105	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__C-114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478725.1	s__C-114 sp015478725	77.7806	142	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__C-114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822495.1	s__CAIJPD01 sp903822495	77.6619	119	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIJPD01	95.0	99.94	99.94	0.97	0.97	2	-
GCA_003152165.1	s__Palsa-1033 sp003152165	77.5532	139	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694835.1	s__JACDBP01 sp013694835	77.3096	59	445	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__JACDBP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:06:52,631] [INFO] GTDB search result was written to GCA_013697965.1_ASM1369796v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:06:52,631] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:06:52,635] [INFO] DFAST_QC result json was written to GCA_013697965.1_ASM1369796v1_genomic.fna/dqc_result.json
[2023-06-19 10:06:52,635] [INFO] DFAST_QC completed!
[2023-06-19 10:06:52,635] [INFO] Total running time: 0h0m50s