[2024-01-24 13:12:35,802] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:35,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:35,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg18b0ab7a-aebb-4d49-b62f-7a7fbfe5922e/dqc_reference
[2024-01-24 13:12:37,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:37,058] [INFO] Task started: Prodigal
[2024-01-24 13:12:37,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f6cf043-e5c9-4bcf-bc6d-7c69eaa2eab7/GCF_019670005.1_ASM1967000v1_genomic.fna.gz | prodigal -d GCF_019670005.1_ASM1967000v1_genomic.fna/cds.fna -a GCF_019670005.1_ASM1967000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:54,444] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:54,445] [INFO] Task started: HMMsearch
[2024-01-24 13:12:54,445] [INFO] Running command: hmmsearch --tblout GCF_019670005.1_ASM1967000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18b0ab7a-aebb-4d49-b62f-7a7fbfe5922e/dqc_reference/reference_markers.hmm GCF_019670005.1_ASM1967000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:54,799] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:54,800] [INFO] Found 6/6 markers.
[2024-01-24 13:12:54,855] [INFO] Query marker FASTA was written to GCF_019670005.1_ASM1967000v1_genomic.fna/markers.fasta
[2024-01-24 13:12:54,855] [INFO] Task started: Blastn
[2024-01-24 13:12:54,855] [INFO] Running command: blastn -query GCF_019670005.1_ASM1967000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b0ab7a-aebb-4d49-b62f-7a7fbfe5922e/dqc_reference/reference_markers.fasta -out GCF_019670005.1_ASM1967000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:55,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:55,724] [INFO] Selected 23 target genomes.
[2024-01-24 13:12:55,724] [INFO] Target genome list was writen to GCF_019670005.1_ASM1967000v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:55,734] [INFO] Task started: fastANI
[2024-01-24 13:12:55,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f6cf043-e5c9-4bcf-bc6d-7c69eaa2eab7/GCF_019670005.1_ASM1967000v1_genomic.fna.gz --refList GCF_019670005.1_ASM1967000v1_genomic.fna/target_genomes.txt --output GCF_019670005.1_ASM1967000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:11,735] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:11,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18b0ab7a-aebb-4d49-b62f-7a7fbfe5922e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:11,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18b0ab7a-aebb-4d49-b62f-7a7fbfe5922e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:11,758] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:11,758] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:11,758] [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
Methylomagnum ishizawai	strain=RS11D-Pr	GCA_019670005.1	1760988	1760988	type	True	100.0	1729	1729	95	conclusive
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	77.9173	308	1729	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	77.7316	310	1729	95	below_threshold
Methylogaea oryzae	strain=JCM 16910	GCA_001312345.1	1295382	1295382	type	True	77.4418	218	1729	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	77.4413	325	1729	95	below_threshold
Methylococcus capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	77.3761	266	1729	95	below_threshold
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	77.1676	263	1729	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.8145	157	1729	95	below_threshold
Methylotetracoccus oryzae	strain=C50C1	GCA_006175985.1	1919059	1919059	type	True	76.638	182	1729	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.4726	150	1729	95	below_threshold
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	76.365	84	1729	95	below_threshold
Acidihalobacter ferrooxydans	strain=V8	GCA_001975725.1	1765967	1765967	type	True	76.2539	85	1729	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	76.1874	114	1729	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	76.1549	128	1729	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.1255	147	1729	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.1143	156	1729	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.0908	83	1729	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.9371	117	1729	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.916	119	1729	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	75.8315	120	1729	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.7078	143	1729	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:11,760] [INFO] DFAST Taxonomy check result was written to GCF_019670005.1_ASM1967000v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:11,761] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:11,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:11,761] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18b0ab7a-aebb-4d49-b62f-7a7fbfe5922e/dqc_reference/checkm_data
[2024-01-24 13:13:11,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:11,810] [INFO] Task started: CheckM
[2024-01-24 13:13:11,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019670005.1_ASM1967000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019670005.1_ASM1967000v1_genomic.fna/checkm_input GCF_019670005.1_ASM1967000v1_genomic.fna/checkm_result
[2024-01-24 13:14:02,603] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:02,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:02,626] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:02,626] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:02,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019670005.1_ASM1967000v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:02,627] [INFO] Task started: Blastn
[2024-01-24 13:14:02,627] [INFO] Running command: blastn -query GCF_019670005.1_ASM1967000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b0ab7a-aebb-4d49-b62f-7a7fbfe5922e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019670005.1_ASM1967000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:04,171] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:04,174] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:04,174] [INFO] Target genome list was writen to GCF_019670005.1_ASM1967000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:04,190] [INFO] Task started: fastANI
[2024-01-24 13:14:04,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f6cf043-e5c9-4bcf-bc6d-7c69eaa2eab7/GCF_019670005.1_ASM1967000v1_genomic.fna.gz --refList GCF_019670005.1_ASM1967000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019670005.1_ASM1967000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:17,217] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:17,242] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:14:17,242] [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_900155475.1	s__Methylomagnum ishizawai	93.5482	1415	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylomagnum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810705.1	s__CADDYU01 sp902810705	78.0248	371	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__CADDYU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012769535.1	s__Methylococcus sp012769535	77.9597	307	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016925495.1	s__EFPC2 sp016925495	77.8539	318	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__EFPC2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934725.1	s__Methyloterricola oryzae	77.7505	309	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026715.1	s__VEPB01 sp012026715	77.5327	260	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__VEPB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001312345.1	s__Methylogaea oryzae	77.4418	218	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylogaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424685.1	s__Methylococcus capsulatus	77.3124	263	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	99.39	98.77	0.98	0.95	3	-
GCF_002005105.1	s__Methylocaldum sp002005105	77.1003	255	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	98.51	98.17	0.91	0.88	6	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	76.813	79	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000299335.2	s__Alcanivorax_A pacificus	76.566	84	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002391525.1	s__Competibacter_A sp002391525	76.3991	157	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Competibacter_A	95.0	99.79	99.79	0.93	0.93	2	-
GCA_008933795.1	s__Contendobacter sp008933795	76.3723	170	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Contendobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	76.1139	148	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711015.1	s__Methylomonas sp015711015	76.016	114	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	75.8875	123	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_011752565.1	s__Pseudomonas_E sp011752565	75.5636	126	1729	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.50	98.50	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:17,244] [INFO] GTDB search result was written to GCF_019670005.1_ASM1967000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:17,244] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:17,248] [INFO] DFAST_QC result json was written to GCF_019670005.1_ASM1967000v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:17,248] [INFO] DFAST_QC completed!
[2024-01-24 13:14:17,248] [INFO] Total running time: 0h1m41s