[2023-06-28 20:40:56,438] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:40:56,444] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:40:56,445] [INFO] DQC Reference Directory: /var/lib/cwl/stge85bee74-8ba8-451b-a14d-16b1b6a17db9/dqc_reference
[2023-06-28 20:40:57,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:40:57,762] [INFO] Task started: Prodigal
[2023-06-28 20:40:57,763] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcce988f-6870-4ac6-90bb-c51b0e2d792e/GCA_027081195.1_ASM2708119v1_genomic.fna.gz | prodigal -d GCA_027081195.1_ASM2708119v1_genomic.fna/cds.fna -a GCA_027081195.1_ASM2708119v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:41:06,016] [INFO] Task succeeded: Prodigal
[2023-06-28 20:41:06,016] [INFO] Task started: HMMsearch
[2023-06-28 20:41:06,016] [INFO] Running command: hmmsearch --tblout GCA_027081195.1_ASM2708119v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge85bee74-8ba8-451b-a14d-16b1b6a17db9/dqc_reference/reference_markers.hmm GCA_027081195.1_ASM2708119v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:41:06,310] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:41:06,317] [INFO] Found 6/6 markers.
[2023-06-28 20:41:06,347] [INFO] Query marker FASTA was written to GCA_027081195.1_ASM2708119v1_genomic.fna/markers.fasta
[2023-06-28 20:41:06,348] [INFO] Task started: Blastn
[2023-06-28 20:41:06,348] [INFO] Running command: blastn -query GCA_027081195.1_ASM2708119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge85bee74-8ba8-451b-a14d-16b1b6a17db9/dqc_reference/reference_markers.fasta -out GCA_027081195.1_ASM2708119v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:41:06,985] [INFO] Task succeeded: Blastn
[2023-06-28 20:41:06,988] [INFO] Selected 15 target genomes.
[2023-06-28 20:41:06,989] [INFO] Target genome list was writen to GCA_027081195.1_ASM2708119v1_genomic.fna/target_genomes.txt
[2023-06-28 20:41:06,990] [INFO] Task started: fastANI
[2023-06-28 20:41:06,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcce988f-6870-4ac6-90bb-c51b0e2d792e/GCA_027081195.1_ASM2708119v1_genomic.fna.gz --refList GCA_027081195.1_ASM2708119v1_genomic.fna/target_genomes.txt --output GCA_027081195.1_ASM2708119v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:41:16,057] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:16,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge85bee74-8ba8-451b-a14d-16b1b6a17db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:41:16,058] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge85bee74-8ba8-451b-a14d-16b1b6a17db9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:41:16,071] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:41:16,071] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:41:16,072] [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
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	77.3288	173	871	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	77.2885	206	871	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	77.1965	164	871	95	below_threshold
Desulfobulbus oralis	strain=HOT041/ORNL	GCA_002952055.1	1986146	1986146	type	True	76.576	60	871	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	76.3174	84	871	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_016918515.1	1506996	1506996	type	True	76.3083	83	871	95	below_threshold
Desulfobulbus rhabdoformis	strain=DSM 8777	GCA_016919065.1	34032	34032	type	True	76.1279	82	871	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:41:16,075] [INFO] DFAST Taxonomy check result was written to GCA_027081195.1_ASM2708119v1_genomic.fna/tc_result.tsv
[2023-06-28 20:41:16,076] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:41:16,076] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:41:16,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge85bee74-8ba8-451b-a14d-16b1b6a17db9/dqc_reference/checkm_data
[2023-06-28 20:41:16,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:41:16,115] [INFO] Task started: CheckM
[2023-06-28 20:41:16,115] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027081195.1_ASM2708119v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027081195.1_ASM2708119v1_genomic.fna/checkm_input GCA_027081195.1_ASM2708119v1_genomic.fna/checkm_result
[2023-06-28 20:41:45,526] [INFO] Task succeeded: CheckM
[2023-06-28 20:41:45,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.86%
Contamintation: 1.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 20:41:45,555] [INFO] ===== Completeness check finished =====
[2023-06-28 20:41:45,555] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:41:45,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027081195.1_ASM2708119v1_genomic.fna/markers.fasta)
[2023-06-28 20:41:45,556] [INFO] Task started: Blastn
[2023-06-28 20:41:45,556] [INFO] Running command: blastn -query GCA_027081195.1_ASM2708119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge85bee74-8ba8-451b-a14d-16b1b6a17db9/dqc_reference/reference_markers_gtdb.fasta -out GCA_027081195.1_ASM2708119v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:41:46,470] [INFO] Task succeeded: Blastn
[2023-06-28 20:41:46,475] [INFO] Selected 25 target genomes.
[2023-06-28 20:41:46,475] [INFO] Target genome list was writen to GCA_027081195.1_ASM2708119v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:41:46,499] [INFO] Task started: fastANI
[2023-06-28 20:41:46,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcce988f-6870-4ac6-90bb-c51b0e2d792e/GCA_027081195.1_ASM2708119v1_genomic.fna.gz --refList GCA_027081195.1_ASM2708119v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027081195.1_ASM2708119v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:41:59,433] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:59,453] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:41:59,453] [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_015484845.1	s__DRKI01 sp015484845	79.1133	341	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051875.1	s__DRKI01 sp011051875	78.3979	281	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	99.14	99.09	0.93	0.90	3	-
GCA_017998195.1	s__Desulfobulbus sp017998195	77.7515	124	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003604995.1	s__UBA10518 sp003604995	77.6733	126	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489765.1	s__DRLX01 sp015489765	77.4062	162	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621145.1	s__Desulfobulbus elongatus	77.3288	173	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151365.1	s__BMS3Abin13 sp013151365	77.309	149	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__BMS3Abin13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429965.1	s__Desulfobulbus_A mediterraneus	77.2885	206	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186885.1	s__Desulfobulbus propionicus	77.1965	164	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015486315.1	s__Desulfobulbus_C sp015486315	77.1921	103	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009782165.1	s__Desulfobulbus sp009782165	77.1174	74	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003508005.1	s__UBA10518 sp003508005	77.0135	152	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051825.1	s__DRLX01 sp011051825	76.7628	158	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873115.1	s__CG2-30-60-27 sp001873115	76.7244	69	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__CG2-30-60-27	95.0	99.49	99.49	0.83	0.83	2	-
GCA_903842475.1	s__Desulfobulbus sp903842475	76.712	100	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009778955.1	s__Desulfobulbus sp009778955	76.6119	102	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163135.1	s__Desulfobulbus sp019163135	76.566	97	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919065.1	s__Desulfobulbus rhabdoformis	76.1279	82	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163335.1	s__UBA2270 sp019163335	76.0891	52	871	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__UBA2270	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:41:59,455] [INFO] GTDB search result was written to GCA_027081195.1_ASM2708119v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:41:59,456] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:41:59,460] [INFO] DFAST_QC result json was written to GCA_027081195.1_ASM2708119v1_genomic.fna/dqc_result.json
[2023-06-28 20:41:59,460] [INFO] DFAST_QC completed!
[2023-06-28 20:41:59,460] [INFO] Total running time: 0h1m3s