[2023-06-29 02:28:46,483] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:28:46,485] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:28:46,485] [INFO] DQC Reference Directory: /var/lib/cwl/stg885944e3-db38-4944-a26c-1a8e6cb2f642/dqc_reference
[2023-06-29 02:28:47,709] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:28:47,710] [INFO] Task started: Prodigal
[2023-06-29 02:28:47,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ee1aff0-34c9-487d-bc6c-a27fda720c0c/GCA_027430195.1_ASM2743019v1_genomic.fna.gz | prodigal -d GCA_027430195.1_ASM2743019v1_genomic.fna/cds.fna -a GCA_027430195.1_ASM2743019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:29:05,872] [INFO] Task succeeded: Prodigal
[2023-06-29 02:29:05,873] [INFO] Task started: HMMsearch
[2023-06-29 02:29:05,873] [INFO] Running command: hmmsearch --tblout GCA_027430195.1_ASM2743019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg885944e3-db38-4944-a26c-1a8e6cb2f642/dqc_reference/reference_markers.hmm GCA_027430195.1_ASM2743019v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:29:06,220] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:29:06,221] [INFO] Found 6/6 markers.
[2023-06-29 02:29:06,283] [INFO] Query marker FASTA was written to GCA_027430195.1_ASM2743019v1_genomic.fna/markers.fasta
[2023-06-29 02:29:06,283] [INFO] Task started: Blastn
[2023-06-29 02:29:06,284] [INFO] Running command: blastn -query GCA_027430195.1_ASM2743019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg885944e3-db38-4944-a26c-1a8e6cb2f642/dqc_reference/reference_markers.fasta -out GCA_027430195.1_ASM2743019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:29:06,954] [INFO] Task succeeded: Blastn
[2023-06-29 02:29:06,959] [INFO] Selected 28 target genomes.
[2023-06-29 02:29:06,959] [INFO] Target genome list was writen to GCA_027430195.1_ASM2743019v1_genomic.fna/target_genomes.txt
[2023-06-29 02:29:06,994] [INFO] Task started: fastANI
[2023-06-29 02:29:06,994] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee1aff0-34c9-487d-bc6c-a27fda720c0c/GCA_027430195.1_ASM2743019v1_genomic.fna.gz --refList GCA_027430195.1_ASM2743019v1_genomic.fna/target_genomes.txt --output GCA_027430195.1_ASM2743019v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:29:34,358] [INFO] Task succeeded: fastANI
[2023-06-29 02:29:34,359] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg885944e3-db38-4944-a26c-1a8e6cb2f642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:29:34,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg885944e3-db38-4944-a26c-1a8e6cb2f642/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:29:34,369] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:29:34,370] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:29:34,370] [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
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.4814	70	1803	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.3765	53	1803	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.2633	98	1803	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.0022	99	1803	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	74.8475	54	1803	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:29:34,372] [INFO] DFAST Taxonomy check result was written to GCA_027430195.1_ASM2743019v1_genomic.fna/tc_result.tsv
[2023-06-29 02:29:34,372] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:29:34,372] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:29:34,373] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg885944e3-db38-4944-a26c-1a8e6cb2f642/dqc_reference/checkm_data
[2023-06-29 02:29:34,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:29:34,432] [INFO] Task started: CheckM
[2023-06-29 02:29:34,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027430195.1_ASM2743019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027430195.1_ASM2743019v1_genomic.fna/checkm_input GCA_027430195.1_ASM2743019v1_genomic.fna/checkm_result
[2023-06-29 02:30:29,406] [INFO] Task succeeded: CheckM
[2023-06-29 02:30:29,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 02:30:29,435] [INFO] ===== Completeness check finished =====
[2023-06-29 02:30:29,435] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:30:29,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027430195.1_ASM2743019v1_genomic.fna/markers.fasta)
[2023-06-29 02:30:29,436] [INFO] Task started: Blastn
[2023-06-29 02:30:29,436] [INFO] Running command: blastn -query GCA_027430195.1_ASM2743019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg885944e3-db38-4944-a26c-1a8e6cb2f642/dqc_reference/reference_markers_gtdb.fasta -out GCA_027430195.1_ASM2743019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:30:30,248] [INFO] Task succeeded: Blastn
[2023-06-29 02:30:30,253] [INFO] Selected 25 target genomes.
[2023-06-29 02:30:30,254] [INFO] Target genome list was writen to GCA_027430195.1_ASM2743019v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:30:30,262] [INFO] Task started: fastANI
[2023-06-29 02:30:30,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ee1aff0-34c9-487d-bc6c-a27fda720c0c/GCA_027430195.1_ASM2743019v1_genomic.fna.gz --refList GCA_027430195.1_ASM2743019v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027430195.1_ASM2743019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:31:02,136] [INFO] Task succeeded: fastANI
[2023-06-29 02:31:02,157] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 02:31:02,157] [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_009691905.1	s__SIAF01 sp009691905	76.0996	161	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200145.1	s__JACQFH01 sp016200145	76.0827	216	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACQFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235885.1	s__JACRIH01 sp016235885	75.8476	118	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACRIH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	75.4539	89	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCA_003508595.1	s__UBA10511 sp003508595	75.4171	65	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__UBA10511	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	75.3867	59	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242525.1	s__Schlesneria sp018242525	75.3751	73	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669125.1	s__SXKJ01 sp003669125	75.2889	66	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.07	98.94	0.92	0.91	3	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.2633	98	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861195.1	s__UBA10511 sp903861195	75.2517	92	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__UBA10511	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903840265.1	s__Schlesneria sp903840265	75.219	53	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	99.98	99.98	0.97	0.97	3	-
GCA_005778115.1	s__SXKJ01 sp005778115	75.2183	60	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.84	99.84	0.89	0.89	2	-
GCA_005798445.1	s__SXKJ01 sp005798445	75.197	62	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.80	99.80	0.90	0.90	2	-
GCA_003389325.1	s__LB-PLM-3 sp003389325	75.1567	89	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__LB-PLM-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	75.1541	51	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_016872645.1	s__SXKJ01 sp016872645	75.1004	60	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	75.0628	75	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752535.1	s__Tautonia plasticadhaerens	75.0019	99	1803	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361685.1	s__Catenulispora sp013361685	74.5285	70	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 02:31:02,159] [INFO] GTDB search result was written to GCA_027430195.1_ASM2743019v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:31:02,160] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:31:02,163] [INFO] DFAST_QC result json was written to GCA_027430195.1_ASM2743019v1_genomic.fna/dqc_result.json
[2023-06-29 02:31:02,163] [INFO] DFAST_QC completed!
[2023-06-29 02:31:02,163] [INFO] Total running time: 0h2m16s