[2024-01-25 20:13:35,541] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:35,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:35,543] [INFO] DQC Reference Directory: /var/lib/cwl/stgc66f3735-251c-4150-8f2c-19854cf4ca3f/dqc_reference
[2024-01-25 20:13:36,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:36,692] [INFO] Task started: Prodigal
[2024-01-25 20:13:36,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg77319f6d-6100-427c-a23a-eb6174063793/GCF_014207595.1_ASM1420759v1_genomic.fna.gz | prodigal -d GCF_014207595.1_ASM1420759v1_genomic.fna/cds.fna -a GCF_014207595.1_ASM1420759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:47,934] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:47,935] [INFO] Task started: HMMsearch
[2024-01-25 20:13:47,935] [INFO] Running command: hmmsearch --tblout GCF_014207595.1_ASM1420759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc66f3735-251c-4150-8f2c-19854cf4ca3f/dqc_reference/reference_markers.hmm GCF_014207595.1_ASM1420759v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:48,180] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:48,181] [INFO] Found 6/6 markers.
[2024-01-25 20:13:48,215] [INFO] Query marker FASTA was written to GCF_014207595.1_ASM1420759v1_genomic.fna/markers.fasta
[2024-01-25 20:13:48,216] [INFO] Task started: Blastn
[2024-01-25 20:13:48,216] [INFO] Running command: blastn -query GCF_014207595.1_ASM1420759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc66f3735-251c-4150-8f2c-19854cf4ca3f/dqc_reference/reference_markers.fasta -out GCF_014207595.1_ASM1420759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:48,910] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:48,913] [INFO] Selected 19 target genomes.
[2024-01-25 20:13:48,913] [INFO] Target genome list was writen to GCF_014207595.1_ASM1420759v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:48,923] [INFO] Task started: fastANI
[2024-01-25 20:13:48,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg77319f6d-6100-427c-a23a-eb6174063793/GCF_014207595.1_ASM1420759v1_genomic.fna.gz --refList GCF_014207595.1_ASM1420759v1_genomic.fna/target_genomes.txt --output GCF_014207595.1_ASM1420759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:04,652] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:04,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc66f3735-251c-4150-8f2c-19854cf4ca3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:04,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc66f3735-251c-4150-8f2c-19854cf4ca3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:04,662] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:04,662] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:04,662] [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
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	100.0	1387	1387	95	conclusive
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	77.5151	137	1387	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	77.3211	270	1387	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	77.292	270	1387	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	76.2324	113	1387	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.3832	101	1387	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	75.3216	54	1387	95	below_threshold
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	75.1855	105	1387	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.1267	51	1387	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.1074	115	1387	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	75.001	82	1387	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.982	71	1387	95	below_threshold
Lentzea kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	74.8739	99	1387	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:04,664] [INFO] DFAST Taxonomy check result was written to GCF_014207595.1_ASM1420759v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:04,664] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:04,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:04,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc66f3735-251c-4150-8f2c-19854cf4ca3f/dqc_reference/checkm_data
[2024-01-25 20:14:04,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:04,707] [INFO] Task started: CheckM
[2024-01-25 20:14:04,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014207595.1_ASM1420759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014207595.1_ASM1420759v1_genomic.fna/checkm_input GCF_014207595.1_ASM1420759v1_genomic.fna/checkm_result
[2024-01-25 20:14:39,392] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:39,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:39,412] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:39,412] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:39,412] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014207595.1_ASM1420759v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:39,413] [INFO] Task started: Blastn
[2024-01-25 20:14:39,413] [INFO] Running command: blastn -query GCF_014207595.1_ASM1420759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc66f3735-251c-4150-8f2c-19854cf4ca3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014207595.1_ASM1420759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:40,520] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:40,524] [INFO] Selected 26 target genomes.
[2024-01-25 20:14:40,524] [INFO] Target genome list was writen to GCF_014207595.1_ASM1420759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:40,544] [INFO] Task started: fastANI
[2024-01-25 20:14:40,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg77319f6d-6100-427c-a23a-eb6174063793/GCF_014207595.1_ASM1420759v1_genomic.fna.gz --refList GCF_014207595.1_ASM1420759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014207595.1_ASM1420759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:02,688] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:02,696] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:02,697] [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_014207595.1	s__Algisphaera agarilytica	100.0	1387	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Algisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007748075.1	s__Pan265 sp007748075	77.5153	137	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Pan265	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284115.1	s__Phycisphaera mikurensis	77.2807	271	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Phycisphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCA_016125215.1	s__RI-382 sp016125215	76.9655	198	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__RI-382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125285.1	s__RI-212 sp016125285	76.7851	176	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Zrk34;g__RI-212	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873095.1	s__Zrk34 sp014873095	76.7761	147	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Zrk34;g__Zrk34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551485.1	s__B1Sed10-187 sp003551485	76.6362	121	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__B1Sed10-187	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125255.1	s__RI-421 sp016125255	76.4339	160	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Zrk34;g__RI-421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119405.1	s__SKPT01 sp007119405	76.4059	110	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__SKPT01	95.0	98.45	98.45	0.84	0.84	2	-
GCA_903891095.1	s__QWPT01 sp903891095	76.3502	104	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.40	98.92	0.94	0.91	5	-
GCA_002686995.1	s__GCA-2686995 sp002686995	76.1953	136	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__GCA-2686995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008363215.1	s__J022 sp008363215	76.0824	61	1387	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J022	95.0	99.97	99.97	0.97	0.97	2	-
GCA_016717595.1	s__JADKFE01 sp016717595	75.0186	72	1387	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:02,698] [INFO] GTDB search result was written to GCF_014207595.1_ASM1420759v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:02,699] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:02,702] [INFO] DFAST_QC result json was written to GCF_014207595.1_ASM1420759v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:02,702] [INFO] DFAST_QC completed!
[2024-01-25 20:15:02,702] [INFO] Total running time: 0h1m27s