[2024-01-24 10:47:06,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f139721-d0e5-466a-8440-d4c84b044121/dqc_reference
[2024-01-24 10:47:12,682] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,828] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg24c8c98a-415f-44ce-b365-0195639ec9c4/GCF_024256385.1_ASM2425638v1_genomic.fna.gz | prodigal -d GCF_024256385.1_ASM2425638v1_genomic.fna/cds.fna -a GCF_024256385.1_ASM2425638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:00,292] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:00,292] [INFO] Task started: HMMsearch
[2024-01-24 10:48:00,292] [INFO] Running command: hmmsearch --tblout GCF_024256385.1_ASM2425638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f139721-d0e5-466a-8440-d4c84b044121/dqc_reference/reference_markers.hmm GCF_024256385.1_ASM2425638v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:00,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:00,705] [INFO] Found 6/6 markers.
[2024-01-24 10:48:00,777] [INFO] Query marker FASTA was written to GCF_024256385.1_ASM2425638v1_genomic.fna/markers.fasta
[2024-01-24 10:48:00,777] [INFO] Task started: Blastn
[2024-01-24 10:48:00,778] [INFO] Running command: blastn -query GCF_024256385.1_ASM2425638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f139721-d0e5-466a-8440-d4c84b044121/dqc_reference/reference_markers.fasta -out GCF_024256385.1_ASM2425638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:01,373] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:01,376] [INFO] Selected 19 target genomes.
[2024-01-24 10:48:01,377] [INFO] Target genome list was writen to GCF_024256385.1_ASM2425638v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:01,599] [INFO] Task started: fastANI
[2024-01-24 10:48:01,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg24c8c98a-415f-44ce-b365-0195639ec9c4/GCF_024256385.1_ASM2425638v1_genomic.fna.gz --refList GCF_024256385.1_ASM2425638v1_genomic.fna/target_genomes.txt --output GCF_024256385.1_ASM2425638v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:24,794] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:24,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f139721-d0e5-466a-8440-d4c84b044121/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:24,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f139721-d0e5-466a-8440-d4c84b044121/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:24,815] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:24,815] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:24,815] [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
Anatilimnocola aggregata	strain=ETA_A8	GCA_007747655.1	2528021	2528021	type	True	77.9305	790	2972	95	below_threshold
Pirellula staleyi	strain=DSM 6068	GCA_000025185.1	125	125	type	True	76.6625	221	2972	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	76.056	145	2972	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.0526	164	2972	95	below_threshold
Bremerella volcania	strain=Pan97	GCA_007748115.1	2527984	2527984	type	True	76.0099	108	2972	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	75.9001	59	2972	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	75.8814	56	2972	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	75.8595	63	2972	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.7897	91	2972	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	75.7644	55	2972	95	below_threshold
Rosistilla ulvae	strain=EC9	GCA_007741475.1	1930277	1930277	type	True	75.7175	100	2972	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.6872	161	2972	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.6806	105	2972	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	75.5867	60	2972	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	75.5753	88	2972	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	75.5738	69	2972	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	75.4877	68	2972	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	75.4481	72	2972	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	75.3791	50	2972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:24,817] [INFO] DFAST Taxonomy check result was written to GCF_024256385.1_ASM2425638v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:24,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:24,818] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:24,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f139721-d0e5-466a-8440-d4c84b044121/dqc_reference/checkm_data
[2024-01-24 10:48:24,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:24,904] [INFO] Task started: CheckM
[2024-01-24 10:48:24,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024256385.1_ASM2425638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024256385.1_ASM2425638v1_genomic.fna/checkm_input GCF_024256385.1_ASM2425638v1_genomic.fna/checkm_result
[2024-01-24 10:50:29,740] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:29,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:29,772] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:29,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:29,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024256385.1_ASM2425638v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:29,773] [INFO] Task started: Blastn
[2024-01-24 10:50:29,773] [INFO] Running command: blastn -query GCF_024256385.1_ASM2425638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f139721-d0e5-466a-8440-d4c84b044121/dqc_reference/reference_markers_gtdb.fasta -out GCF_024256385.1_ASM2425638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:30,638] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:30,642] [INFO] Selected 23 target genomes.
[2024-01-24 10:50:30,643] [INFO] Target genome list was writen to GCF_024256385.1_ASM2425638v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:30,668] [INFO] Task started: fastANI
[2024-01-24 10:50:30,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg24c8c98a-415f-44ce-b365-0195639ec9c4/GCF_024256385.1_ASM2425638v1_genomic.fna.gz --refList GCF_024256385.1_ASM2425638v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024256385.1_ASM2425638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:57,034] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:57,057] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:50:57,058] [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_007747655.1	s__Anatilimnocola aggregata	77.9394	788	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Anatilimnocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025185.1	s__Pirellula staleyi	76.6722	220	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Pirellula	95.0	98.27	98.27	0.94	0.94	2	-
GCF_007859755.1	s__Blastopirellula retiformator	76.0407	145	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Blastopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303535.1	s__PNKZ01 sp017303535	76.0049	176	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__PNKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778405.1	s__SXOA01 sp005778405	75.9092	198	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SXOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860095.1	s__Novipirellula galeiformis	75.8814	56	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	75.8722	119	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002967715.1	s__Bremerella marina_B	75.772	97	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Bremerella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016793115.1	s__PNKZ01 sp016793115	75.7673	203	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__PNKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	75.744	56	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191115.1	s__JACPPG01 sp016191115	75.7406	119	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACPPG01;g__JACPPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576845.1	s__PLA5 sp003576845	75.7314	170	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PLA5;g__PLA5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007751035.1	s__Lignipirellula cremea	75.673	161	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Lignipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242585.1	s__JAFEBQ01 sp018242585	75.6643	146	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__JAFEBQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	75.5867	60	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCA_007753675.1	s__Stieleria sp007753675	75.568	96	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	75.4931	68	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729315.1	s__JAAYDI01 sp012729315	75.4778	65	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__JAAYDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859915.1	s__Rhodopirellula pilleata	75.4619	71	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200205.1	s__PALSA-1355 sp016200205	75.3954	88	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__PALSA-1355	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	75.3648	51	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121535.1	s__SKKK01 sp007121535	75.0724	66	2972	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SKKK01	95.0	99.67	99.63	0.89	0.86	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:57,060] [INFO] GTDB search result was written to GCF_024256385.1_ASM2425638v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:57,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:57,066] [INFO] DFAST_QC result json was written to GCF_024256385.1_ASM2425638v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:57,066] [INFO] DFAST_QC completed!
[2024-01-24 10:50:57,066] [INFO] Total running time: 0h3m50s