[2024-01-24 12:13:05,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:05,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:05,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg9185c878-2d68-4f3e-95a6-c404d00a79fb/dqc_reference
[2024-01-24 12:13:07,172] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:07,173] [INFO] Task started: Prodigal
[2024-01-24 12:13:07,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg528bb071-8ebe-4d54-8a9f-c2e1e55f834d/GCF_007741495.1_ASM774149v1_genomic.fna.gz | prodigal -d GCF_007741495.1_ASM774149v1_genomic.fna/cds.fna -a GCF_007741495.1_ASM774149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:31,674] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:31,675] [INFO] Task started: HMMsearch
[2024-01-24 12:13:31,675] [INFO] Running command: hmmsearch --tblout GCF_007741495.1_ASM774149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9185c878-2d68-4f3e-95a6-c404d00a79fb/dqc_reference/reference_markers.hmm GCF_007741495.1_ASM774149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:31,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:31,981] [INFO] Found 6/6 markers.
[2024-01-24 12:13:32,031] [INFO] Query marker FASTA was written to GCF_007741495.1_ASM774149v1_genomic.fna/markers.fasta
[2024-01-24 12:13:32,031] [INFO] Task started: Blastn
[2024-01-24 12:13:32,031] [INFO] Running command: blastn -query GCF_007741495.1_ASM774149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9185c878-2d68-4f3e-95a6-c404d00a79fb/dqc_reference/reference_markers.fasta -out GCF_007741495.1_ASM774149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:32,601] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:32,605] [INFO] Selected 20 target genomes.
[2024-01-24 12:13:32,605] [INFO] Target genome list was writen to GCF_007741495.1_ASM774149v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:32,640] [INFO] Task started: fastANI
[2024-01-24 12:13:32,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg528bb071-8ebe-4d54-8a9f-c2e1e55f834d/GCF_007741495.1_ASM774149v1_genomic.fna.gz --refList GCF_007741495.1_ASM774149v1_genomic.fna/target_genomes.txt --output GCF_007741495.1_ASM774149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:55,124] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:55,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9185c878-2d68-4f3e-95a6-c404d00a79fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:55,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9185c878-2d68-4f3e-95a6-c404d00a79fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:55,136] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:55,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:55,137] [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
Roseimaritima multifibrata	strain=FF011L	GCA_007741495.1	1930274	1930274	type	True	100.0	2405	2405	95	conclusive
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	77.0547	148	2405	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	77.032	292	2405	95	below_threshold
Roseimaritima ulvae	strain=UC8	GCA_008065135.1	980254	980254	type	True	77.0154	297	2405	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	77.0066	124	2405	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.6004	98	2405	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	76.514	109	2405	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	76.5109	245	2405	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	76.3444	97	2405	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	76.2589	111	2405	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	76.2186	112	2405	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	76.0614	95	2405	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.0429	91	2405	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	76.0025	89	2405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:55,139] [INFO] DFAST Taxonomy check result was written to GCF_007741495.1_ASM774149v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:55,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:55,139] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:55,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9185c878-2d68-4f3e-95a6-c404d00a79fb/dqc_reference/checkm_data
[2024-01-24 12:13:55,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:55,204] [INFO] Task started: CheckM
[2024-01-24 12:13:55,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007741495.1_ASM774149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007741495.1_ASM774149v1_genomic.fna/checkm_input GCF_007741495.1_ASM774149v1_genomic.fna/checkm_result
[2024-01-24 12:15:05,032] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:05,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,058] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:05,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:05,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007741495.1_ASM774149v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:05,059] [INFO] Task started: Blastn
[2024-01-24 12:15:05,059] [INFO] Running command: blastn -query GCF_007741495.1_ASM774149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9185c878-2d68-4f3e-95a6-c404d00a79fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007741495.1_ASM774149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:05,930] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:05,935] [INFO] Selected 22 target genomes.
[2024-01-24 12:15:05,936] [INFO] Target genome list was writen to GCF_007741495.1_ASM774149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:05,961] [INFO] Task started: fastANI
[2024-01-24 12:15:05,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg528bb071-8ebe-4d54-8a9f-c2e1e55f834d/GCF_007741495.1_ASM774149v1_genomic.fna.gz --refList GCF_007741495.1_ASM774149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007741495.1_ASM774149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:37,099] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:37,113] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:37,113] [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_007741495.1	s__Roseimaritima sp007741495	100.0	2405	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008065135.1	s__Roseimaritima ulvae	77.0122	296	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	99.98	99.98	1.00	1.00	2	-
GCF_007860095.1	s__Novipirellula galeiformis	76.9915	144	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	76.6004	98	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCA_007859835.1	s__Novipirellula sp007859835	76.5757	83	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009618275.1	s__Roseimaritima sp009618275	76.5152	242	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	76.4613	108	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741555.1	s__K23-9 sp007741555	76.3593	108	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	76.3027	139	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860175.1	s__Rubripirellula reticaptiva	76.2485	111	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	76.2404	109	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	76.231	96	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694185.1	s__UBA6163 sp007694185	76.0336	68	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	76.0188	88	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_002289565.1	s__Stieleria sp002289565	75.8529	115	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901265.1	s__Stieleria baltica_A	75.6373	98	2405	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:37,115] [INFO] GTDB search result was written to GCF_007741495.1_ASM774149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:37,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:37,120] [INFO] DFAST_QC result json was written to GCF_007741495.1_ASM774149v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:37,120] [INFO] DFAST_QC completed!
[2024-01-24 12:15:37,120] [INFO] Total running time: 0h2m31s