[2024-01-24 12:57:50,119] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:57:50,121] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:57:50,122] [INFO] DQC Reference Directory: /var/lib/cwl/stg8519fb1b-e7c6-4874-9199-ea6cc8493c79/dqc_reference
[2024-01-24 12:57:51,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:57:51,275] [INFO] Task started: Prodigal
[2024-01-24 12:57:51,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d6e6d30-8fc3-4e5a-9920-2a8cb575a1b3/GCF_000346295.1_ASM34629v1_genomic.fna.gz | prodigal -d GCF_000346295.1_ASM34629v1_genomic.fna/cds.fna -a GCF_000346295.1_ASM34629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:58:17,681] [INFO] Task succeeded: Prodigal
[2024-01-24 12:58:17,682] [INFO] Task started: HMMsearch
[2024-01-24 12:58:17,682] [INFO] Running command: hmmsearch --tblout GCF_000346295.1_ASM34629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8519fb1b-e7c6-4874-9199-ea6cc8493c79/dqc_reference/reference_markers.hmm GCF_000346295.1_ASM34629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:58:17,989] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:58:17,991] [INFO] Found 6/6 markers.
[2024-01-24 12:58:18,055] [INFO] Query marker FASTA was written to GCF_000346295.1_ASM34629v1_genomic.fna/markers.fasta
[2024-01-24 12:58:18,055] [INFO] Task started: Blastn
[2024-01-24 12:58:18,055] [INFO] Running command: blastn -query GCF_000346295.1_ASM34629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8519fb1b-e7c6-4874-9199-ea6cc8493c79/dqc_reference/reference_markers.fasta -out GCF_000346295.1_ASM34629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:58:18,625] [INFO] Task succeeded: Blastn
[2024-01-24 12:58:18,629] [INFO] Selected 20 target genomes.
[2024-01-24 12:58:18,629] [INFO] Target genome list was writen to GCF_000346295.1_ASM34629v1_genomic.fna/target_genomes.txt
[2024-01-24 12:58:18,636] [INFO] Task started: fastANI
[2024-01-24 12:58:18,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d6e6d30-8fc3-4e5a-9920-2a8cb575a1b3/GCF_000346295.1_ASM34629v1_genomic.fna.gz --refList GCF_000346295.1_ASM34629v1_genomic.fna/target_genomes.txt --output GCF_000346295.1_ASM34629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:58:43,981] [INFO] Task succeeded: fastANI
[2024-01-24 12:58:43,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8519fb1b-e7c6-4874-9199-ea6cc8493c79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:58:43,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8519fb1b-e7c6-4874-9199-ea6cc8493c79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:58:43,994] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:58:43,995] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:58:43,995] [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
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	100.0	2386	2407	95	conclusive
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	79.4617	784	2407	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	77.5557	175	2407	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.3809	166	2407	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	77.3654	167	2407	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	77.1443	190	2407	95	below_threshold
Novipirellula aureliae	strain=Q31b	GCA_007860185.1	2527966	2527966	type	True	76.9675	180	2407	95	below_threshold
Novipirellula artificiosorum	strain=Poly41	GCA_007860135.1	2528016	2528016	type	True	76.8759	228	2407	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.7627	169	2407	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.7249	253	2407	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	76.6665	236	2407	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	76.6444	154	2407	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	76.6302	161	2407	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.3186	180	2407	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.1525	212	2407	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.9198	127	2407	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:58:43,996] [INFO] DFAST Taxonomy check result was written to GCF_000346295.1_ASM34629v1_genomic.fna/tc_result.tsv
[2024-01-24 12:58:43,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:58:43,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:58:43,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8519fb1b-e7c6-4874-9199-ea6cc8493c79/dqc_reference/checkm_data
[2024-01-24 12:58:43,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:58:44,076] [INFO] Task started: CheckM
[2024-01-24 12:58:44,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000346295.1_ASM34629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000346295.1_ASM34629v1_genomic.fna/checkm_input GCF_000346295.1_ASM34629v1_genomic.fna/checkm_result
[2024-01-24 12:59:59,473] [INFO] Task succeeded: CheckM
[2024-01-24 12:59:59,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.84%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:59:59,501] [INFO] ===== Completeness check finished =====
[2024-01-24 12:59:59,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:59:59,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000346295.1_ASM34629v1_genomic.fna/markers.fasta)
[2024-01-24 12:59:59,502] [INFO] Task started: Blastn
[2024-01-24 12:59:59,502] [INFO] Running command: blastn -query GCF_000346295.1_ASM34629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8519fb1b-e7c6-4874-9199-ea6cc8493c79/dqc_reference/reference_markers_gtdb.fasta -out GCF_000346295.1_ASM34629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:00:00,262] [INFO] Task succeeded: Blastn
[2024-01-24 13:00:00,266] [INFO] Selected 16 target genomes.
[2024-01-24 13:00:00,266] [INFO] Target genome list was writen to GCF_000346295.1_ASM34629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:00:00,353] [INFO] Task started: fastANI
[2024-01-24 13:00:00,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d6e6d30-8fc3-4e5a-9920-2a8cb575a1b3/GCF_000346295.1_ASM34629v1_genomic.fna.gz --refList GCF_000346295.1_ASM34629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000346295.1_ASM34629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:00:24,382] [INFO] Task succeeded: fastANI
[2024-01-24 13:00:24,396] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:00:24,396] [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_000346295.1	s__Novipirellula maiorica	100.0	2386	2407	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_007860095.1	s__Novipirellula galeiformis	79.474	782	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859915.1	s__Rhodopirellula pilleata	77.5554	175	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	77.3654	167	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_007752935.1	s__Crateriforma conspicua	77.3632	167	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_014192335.1	s__Rhodopirellula rubra	77.1934	188	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCA_007859835.1	s__Novipirellula sp007859835	77.0675	227	2407	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	76.9666	179	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860135.1	s__Novipirellula artificiosorum	76.886	227	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	76.8414	224	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	76.7331	252	2407	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	76.6663	236	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196115.1	s__Rhodopirellula baltica	76.6435	160	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCA_007753675.1	s__Stieleria sp007753675	76.4738	222	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	76.4512	226	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741495.1	s__Roseimaritima sp007741495	76.3053	100	2407	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:00:24,397] [INFO] GTDB search result was written to GCF_000346295.1_ASM34629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:00:24,398] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:00:24,401] [INFO] DFAST_QC result json was written to GCF_000346295.1_ASM34629v1_genomic.fna/dqc_result.json
[2024-01-24 13:00:24,402] [INFO] DFAST_QC completed!
[2024-01-24 13:00:24,402] [INFO] Total running time: 0h2m34s