[2024-01-24 10:47:40,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,975] [INFO] DQC Reference Directory: /var/lib/cwl/stgb98055b4-6b03-4939-8de8-a363eb9b4bf8/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,790] [INFO] Running command: gunzip -c /var/lib/cwl/stgf68783b6-f8b1-4db4-934f-5922f56e016e/GCF_019464535.1_ASM1946453v1_genomic.fna.gz | prodigal -d GCF_019464535.1_ASM1946453v1_genomic.fna/cds.fna -a GCF_019464535.1_ASM1946453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:18,880] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:18,880] [INFO] Task started: HMMsearch
[2024-01-24 10:48:18,880] [INFO] Running command: hmmsearch --tblout GCF_019464535.1_ASM1946453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb98055b4-6b03-4939-8de8-a363eb9b4bf8/dqc_reference/reference_markers.hmm GCF_019464535.1_ASM1946453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:19,146] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:19,147] [INFO] Found 6/6 markers.
[2024-01-24 10:48:19,181] [INFO] Query marker FASTA was written to GCF_019464535.1_ASM1946453v1_genomic.fna/markers.fasta
[2024-01-24 10:48:19,182] [INFO] Task started: Blastn
[2024-01-24 10:48:19,182] [INFO] Running command: blastn -query GCF_019464535.1_ASM1946453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb98055b4-6b03-4939-8de8-a363eb9b4bf8/dqc_reference/reference_markers.fasta -out GCF_019464535.1_ASM1946453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:19,903] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:19,906] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:19,907] [INFO] Target genome list was writen to GCF_019464535.1_ASM1946453v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:19,912] [INFO] Task started: fastANI
[2024-01-24 10:48:19,912] [INFO] Running command: fastANI --query /var/lib/cwl/stgf68783b6-f8b1-4db4-934f-5922f56e016e/GCF_019464535.1_ASM1946453v1_genomic.fna.gz --refList GCF_019464535.1_ASM1946453v1_genomic.fna/target_genomes.txt --output GCF_019464535.1_ASM1946453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:27,535] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:27,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb98055b4-6b03-4939-8de8-a363eb9b4bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:27,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb98055b4-6b03-4939-8de8-a363eb9b4bf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:27,546] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:27,546] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:27,546] [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
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.5533	282	1440	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.5334	320	1440	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.2553	219	1440	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.2415	160	1440	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	76.9903	159	1440	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.9575	159	1440	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	74.8923	71	1440	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.8874	72	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:27,548] [INFO] DFAST Taxonomy check result was written to GCF_019464535.1_ASM1946453v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:27,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:27,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:27,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb98055b4-6b03-4939-8de8-a363eb9b4bf8/dqc_reference/checkm_data
[2024-01-24 10:48:27,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:27,598] [INFO] Task started: CheckM
[2024-01-24 10:48:27,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019464535.1_ASM1946453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019464535.1_ASM1946453v1_genomic.fna/checkm_input GCF_019464535.1_ASM1946453v1_genomic.fna/checkm_result
[2024-01-24 10:50:00,911] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:00,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:00,935] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:00,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:00,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019464535.1_ASM1946453v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:00,937] [INFO] Task started: Blastn
[2024-01-24 10:50:00,937] [INFO] Running command: blastn -query GCF_019464535.1_ASM1946453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb98055b4-6b03-4939-8de8-a363eb9b4bf8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019464535.1_ASM1946453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:02,322] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:02,326] [INFO] Selected 27 target genomes.
[2024-01-24 10:50:02,327] [INFO] Target genome list was writen to GCF_019464535.1_ASM1946453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:02,448] [INFO] Task started: fastANI
[2024-01-24 10:50:02,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgf68783b6-f8b1-4db4-934f-5922f56e016e/GCF_019464535.1_ASM1946453v1_genomic.fna.gz --refList GCF_019464535.1_ASM1946453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019464535.1_ASM1946453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:22,508] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:22,534] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:50:22,534] [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_903839035.1	s__Opi-474 sp903839035	77.9949	303	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.67	99.48	0.93	0.89	8	-
GCA_903872505.1	s__Opi-474 sp903872505	77.9565	297	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_018239845.1	s__Opitutus sp018239845	77.8473	379	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859715.1	s__Opi-474 sp903859715	77.8376	290	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.98	99.96	0.98	0.96	7	-
GCA_016794785.1	s__ER46 sp016794785	77.8364	334	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715765.1	s__UBA2377 sp016715765	77.7946	290	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235555.1	s__ER46 sp016235555	77.7835	399	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903855985.1	s__Opi-474 sp903855985	77.7501	304	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903830425.1	s__Opi-474 sp903830425	77.7496	283	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_903862955.1	s__Opi-474 sp903862955	77.696	334	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.96	99.95	0.97	0.97	5	-
GCA_009695305.1	s__CAITWF01 sp009695305	77.656	278	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	77.6489	278	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903948415.1	s__CAITWF01 sp903948415	77.622	327	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002310495.1	s__Nibricoccus aquaticus	77.5798	279	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304445.1	s__Tous-C4FEB sp002304445	77.5678	219	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.22	97.15	0.85	0.81	4	-
GCA_903881475.1	s__Opi-474 sp903881475	77.5657	280	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCA_014376585.1	s__Tous-C4FEB sp014376585	77.5343	310	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019965.1	s__Opitutus terrae	77.5239	321	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003402695.1	s__Opi-474 sp003402695	77.502	254	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795565.1	s__Lacunisphaera sp016795565	77.3964	225	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737275.1	s__Tous-C4FEB sp002737275	77.2721	164	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794665.1	s__ER46 sp016794665	77.2407	270	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054705.1	s__ER46 sp003054705	77.2032	295	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793535.1	s__ER46 sp016793535	77.1272	255	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209255.1	s__ER46 sp016209255	77.0456	237	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919985.1	s__Tous-C4FEB sp903919985	76.9233	140	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903820035.1	s__ER46 sp903820035	76.8766	232	1440	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.61	99.58	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:22,536] [INFO] GTDB search result was written to GCF_019464535.1_ASM1946453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:22,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:22,540] [INFO] DFAST_QC result json was written to GCF_019464535.1_ASM1946453v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:22,541] [INFO] DFAST_QC completed!
[2024-01-24 10:50:22,541] [INFO] Total running time: 0h2m42s