[2024-01-24 13:13:39,103] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:39,104] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:39,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b52963f-c707-4153-9e6c-b469fb3604be/dqc_reference
[2024-01-24 13:13:40,349] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:40,350] [INFO] Task started: Prodigal
[2024-01-24 13:13:40,351] [INFO] Running command: gunzip -c /var/lib/cwl/stg22880273-0fa9-4f3f-9354-9adcc1273133/GCF_001642915.1_ASM164291v1_genomic.fna.gz | prodigal -d GCF_001642915.1_ASM164291v1_genomic.fna/cds.fna -a GCF_001642915.1_ASM164291v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:14:11,008] [INFO] Task succeeded: Prodigal
[2024-01-24 13:14:11,008] [INFO] Task started: HMMsearch
[2024-01-24 13:14:11,009] [INFO] Running command: hmmsearch --tblout GCF_001642915.1_ASM164291v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b52963f-c707-4153-9e6c-b469fb3604be/dqc_reference/reference_markers.hmm GCF_001642915.1_ASM164291v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:14:11,362] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:14:11,364] [INFO] Found 6/6 markers.
[2024-01-24 13:14:11,420] [INFO] Query marker FASTA was written to GCF_001642915.1_ASM164291v1_genomic.fna/markers.fasta
[2024-01-24 13:14:11,421] [INFO] Task started: Blastn
[2024-01-24 13:14:11,421] [INFO] Running command: blastn -query GCF_001642915.1_ASM164291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b52963f-c707-4153-9e6c-b469fb3604be/dqc_reference/reference_markers.fasta -out GCF_001642915.1_ASM164291v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:12,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:12,038] [INFO] Selected 16 target genomes.
[2024-01-24 13:14:12,039] [INFO] Target genome list was writen to GCF_001642915.1_ASM164291v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:12,044] [INFO] Task started: fastANI
[2024-01-24 13:14:12,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg22880273-0fa9-4f3f-9354-9adcc1273133/GCF_001642915.1_ASM164291v1_genomic.fna.gz --refList GCF_001642915.1_ASM164291v1_genomic.fna/target_genomes.txt --output GCF_001642915.1_ASM164291v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:35,669] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:35,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b52963f-c707-4153-9e6c-b469fb3604be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:35,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b52963f-c707-4153-9e6c-b469fb3604be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:35,680] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:35,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:35,680] [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 ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	100.0	2657	2661	95	conclusive
Roseimaritima ulvae	strain=UC8	GCA_008065135.1	980254	980254	type	True	99.9801	2657	2661	95	conclusive
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	78.589	784	2661	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	77.1693	191	2661	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.1283	170	2661	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.1021	199	2661	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	77.0501	147	2661	95	below_threshold
Roseimaritima multifibrata	strain=FF011L	GCA_007741495.1	1930274	1930274	type	True	76.8383	289	2661	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.4774	293	2661	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.3624	193	2661	95	below_threshold
Rosistilla oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	76.1456	196	2661	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	74.6596	75	2661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:35,682] [INFO] DFAST Taxonomy check result was written to GCF_001642915.1_ASM164291v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:35,682] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:35,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:35,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b52963f-c707-4153-9e6c-b469fb3604be/dqc_reference/checkm_data
[2024-01-24 13:14:35,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:35,758] [INFO] Task started: CheckM
[2024-01-24 13:14:35,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001642915.1_ASM164291v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001642915.1_ASM164291v1_genomic.fna/checkm_input GCF_001642915.1_ASM164291v1_genomic.fna/checkm_result
[2024-01-24 13:15:55,913] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:55,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:55,932] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:55,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:55,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001642915.1_ASM164291v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:55,933] [INFO] Task started: Blastn
[2024-01-24 13:15:55,933] [INFO] Running command: blastn -query GCF_001642915.1_ASM164291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b52963f-c707-4153-9e6c-b469fb3604be/dqc_reference/reference_markers_gtdb.fasta -out GCF_001642915.1_ASM164291v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:56,775] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:56,778] [INFO] Selected 19 target genomes.
[2024-01-24 13:15:56,778] [INFO] Target genome list was writen to GCF_001642915.1_ASM164291v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:56,824] [INFO] Task started: fastANI
[2024-01-24 13:15:56,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg22880273-0fa9-4f3f-9354-9adcc1273133/GCF_001642915.1_ASM164291v1_genomic.fna.gz --refList GCF_001642915.1_ASM164291v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001642915.1_ASM164291v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:16:19,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:16:19,937] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:16:19,937] [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_008065135.1	s__Roseimaritima ulvae	99.9801	2657	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_009618275.1	s__Roseimaritima sp009618275	78.5793	788	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	77.1551	192	2661	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	77.1024	200	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCA_007741555.1	s__K23-9 sp007741555	77.0378	154	2661	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_007741495.1	s__Roseimaritima sp007741495	76.8493	289	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	76.64	310	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860045.1	s__Stieleria varia	76.3596	193	2661	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	76.1669	224	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007751715.1	s__Rosistilla oblonga	76.1441	196	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	97.20	97.20	0.92	0.92	2	-
GCF_002901265.1	s__Stieleria baltica_A	76.0926	139	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCA_002422955.1	s__UBA6163 sp002422955	75.7631	106	2661	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428205.1	s__UBA6163 sp002428205	75.5957	112	2661	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 13:16:19,939] [INFO] GTDB search result was written to GCF_001642915.1_ASM164291v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:16:19,939] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:16:19,942] [INFO] DFAST_QC result json was written to GCF_001642915.1_ASM164291v1_genomic.fna/dqc_result.json
[2024-01-24 13:16:19,943] [INFO] DFAST_QC completed!
[2024-01-24 13:16:19,943] [INFO] Total running time: 0h2m41s