[2024-01-24 13:17:59,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:59,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:59,235] [INFO] DQC Reference Directory: /var/lib/cwl/stgeabb15b9-6543-47ac-975b-2e3476cbb6b5/dqc_reference
[2024-01-24 13:18:00,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,596] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,597] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6bd3571-9129-422f-a975-fcb0cfa2ae4e/GCF_009601025.1_ASM960102v1_genomic.fna.gz | prodigal -d GCF_009601025.1_ASM960102v1_genomic.fna/cds.fna -a GCF_009601025.1_ASM960102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:15,751] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:15,752] [INFO] Task started: HMMsearch
[2024-01-24 13:18:15,752] [INFO] Running command: hmmsearch --tblout GCF_009601025.1_ASM960102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeabb15b9-6543-47ac-975b-2e3476cbb6b5/dqc_reference/reference_markers.hmm GCF_009601025.1_ASM960102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:16,046] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:16,048] [INFO] Found 6/6 markers.
[2024-01-24 13:18:16,087] [INFO] Query marker FASTA was written to GCF_009601025.1_ASM960102v1_genomic.fna/markers.fasta
[2024-01-24 13:18:16,088] [INFO] Task started: Blastn
[2024-01-24 13:18:16,088] [INFO] Running command: blastn -query GCF_009601025.1_ASM960102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeabb15b9-6543-47ac-975b-2e3476cbb6b5/dqc_reference/reference_markers.fasta -out GCF_009601025.1_ASM960102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:17,026] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:17,029] [INFO] Selected 13 target genomes.
[2024-01-24 13:18:17,030] [INFO] Target genome list was writen to GCF_009601025.1_ASM960102v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:17,047] [INFO] Task started: fastANI
[2024-01-24 13:18:17,047] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6bd3571-9129-422f-a975-fcb0cfa2ae4e/GCF_009601025.1_ASM960102v1_genomic.fna.gz --refList GCF_009601025.1_ASM960102v1_genomic.fna/target_genomes.txt --output GCF_009601025.1_ASM960102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:31,187] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:31,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeabb15b9-6543-47ac-975b-2e3476cbb6b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:31,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeabb15b9-6543-47ac-975b-2e3476cbb6b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:31,199] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:31,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:31,199] [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
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	100.0	1378	1386	95	conclusive
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	81.767	829	1386	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_008630015.1	140057	140057	type	True	81.7373	825	1386	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	81.7252	825	1386	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	81.655	834	1386	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	77.1874	297	1386	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.8793	332	1386	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.361	291	1386	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3332	349	1386	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	76.2236	236	1386	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.1558	158	1386	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	75.8131	170	1386	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	75.6189	220	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:31,200] [INFO] DFAST Taxonomy check result was written to GCF_009601025.1_ASM960102v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:31,201] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:31,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:31,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeabb15b9-6543-47ac-975b-2e3476cbb6b5/dqc_reference/checkm_data
[2024-01-24 13:18:31,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:31,248] [INFO] Task started: CheckM
[2024-01-24 13:18:31,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009601025.1_ASM960102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009601025.1_ASM960102v1_genomic.fna/checkm_input GCF_009601025.1_ASM960102v1_genomic.fna/checkm_result
[2024-01-24 13:19:26,277] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:26,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:26,299] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:26,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:26,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009601025.1_ASM960102v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:26,300] [INFO] Task started: Blastn
[2024-01-24 13:19:26,300] [INFO] Running command: blastn -query GCF_009601025.1_ASM960102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeabb15b9-6543-47ac-975b-2e3476cbb6b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009601025.1_ASM960102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:28,075] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:28,078] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:28,078] [INFO] Target genome list was writen to GCF_009601025.1_ASM960102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:28,091] [INFO] Task started: fastANI
[2024-01-24 13:19:28,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6bd3571-9129-422f-a975-fcb0cfa2ae4e/GCF_009601025.1_ASM960102v1_genomic.fna.gz --refList GCF_009601025.1_ASM960102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009601025.1_ASM960102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:37,011] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:37,023] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:37,023] [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_009601025.1	s__Rhodospira navarrensis	100.0	1378	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014197795.1	s__Rhodospira goensis	81.7425	833	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197855.1	s__Rhodospira marina	81.6945	830	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	100.00	99.99	1.00	1.00	3	-
GCF_900101965.1	s__Rhodospira trueperi	81.2628	718	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	80.5702	716	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	77.1786	298	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	76.882	335	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003675.1	s__JABDIP01 sp013003675	76.2628	206	1386	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:37,024] [INFO] GTDB search result was written to GCF_009601025.1_ASM960102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:37,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:37,028] [INFO] DFAST_QC result json was written to GCF_009601025.1_ASM960102v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:37,028] [INFO] DFAST_QC completed!
[2024-01-24 13:19:37,028] [INFO] Total running time: 0h1m38s