[2024-01-24 13:27:46,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,183] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,183] [INFO] DQC Reference Directory: /var/lib/cwl/stge0553be2-6f0d-4163-b7b4-063b41f5a6de/dqc_reference
[2024-01-24 13:27:47,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,617] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e475180-e7f0-4360-9639-30555af4016e/GCF_007860095.1_ASM786009v1_genomic.fna.gz | prodigal -d GCF_007860095.1_ASM786009v1_genomic.fna/cds.fna -a GCF_007860095.1_ASM786009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:13,982] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:13,982] [INFO] Task started: HMMsearch
[2024-01-24 13:28:13,983] [INFO] Running command: hmmsearch --tblout GCF_007860095.1_ASM786009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0553be2-6f0d-4163-b7b4-063b41f5a6de/dqc_reference/reference_markers.hmm GCF_007860095.1_ASM786009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:14,432] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:14,434] [INFO] Found 6/6 markers.
[2024-01-24 13:28:14,493] [INFO] Query marker FASTA was written to GCF_007860095.1_ASM786009v1_genomic.fna/markers.fasta
[2024-01-24 13:28:14,494] [INFO] Task started: Blastn
[2024-01-24 13:28:14,494] [INFO] Running command: blastn -query GCF_007860095.1_ASM786009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0553be2-6f0d-4163-b7b4-063b41f5a6de/dqc_reference/reference_markers.fasta -out GCF_007860095.1_ASM786009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:15,093] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:15,096] [INFO] Selected 19 target genomes.
[2024-01-24 13:28:15,096] [INFO] Target genome list was writen to GCF_007860095.1_ASM786009v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:15,109] [INFO] Task started: fastANI
[2024-01-24 13:28:15,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e475180-e7f0-4360-9639-30555af4016e/GCF_007860095.1_ASM786009v1_genomic.fna.gz --refList GCF_007860095.1_ASM786009v1_genomic.fna/target_genomes.txt --output GCF_007860095.1_ASM786009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:41,875] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:41,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0553be2-6f0d-4163-b7b4-063b41f5a6de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:41,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0553be2-6f0d-4163-b7b4-063b41f5a6de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:41,895] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:41,895] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:41,895] [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
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	100.0	2453	2457	95	conclusive
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	79.4997	798	2457	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.0609	179	2457	95	below_threshold
Novipirellula aureliae	strain=Q31b	GCA_007860185.1	2527966	2527966	type	True	77.0267	179	2457	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.7701	176	2457	95	below_threshold
Novipirellula artificiosorum	strain=Poly41	GCA_007860135.1	2528016	2528016	type	True	76.6625	254	2457	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	76.6022	181	2457	95	below_threshold
Rubripirellula amarantea	strain=Pla22	GCA_007859865.1	2527999	2527999	type	True	76.5569	158	2457	95	below_threshold
Rosistilla carotiformis	strain=Poly24	GCA_007753095.1	2528017	2528017	type	True	76.5373	139	2457	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	76.4574	146	2457	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.3546	158	2457	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	76.3507	161	2457	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	76.2988	113	2457	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.2984	226	2457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:41,897] [INFO] DFAST Taxonomy check result was written to GCF_007860095.1_ASM786009v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:41,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:41,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:41,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0553be2-6f0d-4163-b7b4-063b41f5a6de/dqc_reference/checkm_data
[2024-01-24 13:28:41,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:41,972] [INFO] Task started: CheckM
[2024-01-24 13:28:41,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007860095.1_ASM786009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007860095.1_ASM786009v1_genomic.fna/checkm_input GCF_007860095.1_ASM786009v1_genomic.fna/checkm_result
[2024-01-24 13:29:54,348] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:54,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:54,370] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:54,370] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:54,371] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007860095.1_ASM786009v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:54,371] [INFO] Task started: Blastn
[2024-01-24 13:29:54,371] [INFO] Running command: blastn -query GCF_007860095.1_ASM786009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0553be2-6f0d-4163-b7b4-063b41f5a6de/dqc_reference/reference_markers_gtdb.fasta -out GCF_007860095.1_ASM786009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:55,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:55,192] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:55,192] [INFO] Target genome list was writen to GCF_007860095.1_ASM786009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:55,204] [INFO] Task started: fastANI
[2024-01-24 13:29:55,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e475180-e7f0-4360-9639-30555af4016e/GCF_007860095.1_ASM786009v1_genomic.fna.gz --refList GCF_007860095.1_ASM786009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007860095.1_ASM786009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:20,257] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:20,282] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:20,283] [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_007860095.1	s__Novipirellula galeiformis	100.0	2453	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000346295.1	s__Novipirellula maiorica	79.4767	802	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859835.1	s__Novipirellula sp007859835	77.1128	241	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860185.1	s__Novipirellula aureliae	77.0267	179	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192335.1	s__Rhodopirellula rubra	76.7952	158	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_000338295.1	s__Rhodopirellula europaea	76.7442	178	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCA_007753675.1	s__Stieleria sp007753675	76.671	219	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860135.1	s__Novipirellula artificiosorum	76.6625	254	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859865.1	s__Rubripirellula amarantea	76.5332	157	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	76.489	145	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	76.3708	157	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_008312935.1	s__Stieleria lacunae	76.2988	113	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002901265.1	s__Stieleria baltica_A	76.2656	125	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_007754155.1	s__Stieleria neptunia	76.2108	226	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010367455.1	s__Laterigemmans baculatus	75.8084	97	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003506095.1	s__UBA6163 sp003506095	75.7147	65	2457	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:20,285] [INFO] GTDB search result was written to GCF_007860095.1_ASM786009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:20,286] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:20,290] [INFO] DFAST_QC result json was written to GCF_007860095.1_ASM786009v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:20,290] [INFO] DFAST_QC completed!
[2024-01-24 13:30:20,290] [INFO] Total running time: 0h2m34s