[2023-06-29 16:14:59,892] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:14:59,895] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:14:59,895] [INFO] DQC Reference Directory: /var/lib/cwl/stg9960ebc2-441f-45d6-b24b-65684307df59/dqc_reference
[2023-06-29 16:15:01,167] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:15:01,168] [INFO] Task started: Prodigal
[2023-06-29 16:15:01,169] [INFO] Running command: gunzip -c /var/lib/cwl/stge56f5cc2-78a0-4d40-86be-275c1332c69e/GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:15:18,145] [INFO] Task succeeded: Prodigal
[2023-06-29 16:15:18,146] [INFO] Task started: HMMsearch
[2023-06-29 16:15:18,146] [INFO] Running command: hmmsearch --tblout GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9960ebc2-441f-45d6-b24b-65684307df59/dqc_reference/reference_markers.hmm GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:15:18,501] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:15:18,503] [INFO] Found 6/6 markers.
[2023-06-29 16:15:18,572] [INFO] Query marker FASTA was written to GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:15:18,572] [INFO] Task started: Blastn
[2023-06-29 16:15:18,573] [INFO] Running command: blastn -query GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9960ebc2-441f-45d6-b24b-65684307df59/dqc_reference/reference_markers.fasta -out GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:15:19,201] [INFO] Task succeeded: Blastn
[2023-06-29 16:15:19,206] [INFO] Selected 26 target genomes.
[2023-06-29 16:15:19,207] [INFO] Target genome list was writen to GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:15:19,211] [INFO] Task started: fastANI
[2023-06-29 16:15:19,212] [INFO] Running command: fastANI --query /var/lib/cwl/stge56f5cc2-78a0-4d40-86be-275c1332c69e/GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:15:43,142] [INFO] Task succeeded: fastANI
[2023-06-29 16:15:43,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9960ebc2-441f-45d6-b24b-65684307df59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:15:43,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9960ebc2-441f-45d6-b24b-65684307df59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:15:43,158] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:15:43,158] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:15:43,159] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	76.3802	278	1966	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	76.226	163	1966	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	76.2124	134	1966	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.9879	68	1966	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	75.8458	107	1966	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.705	98	1966	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.6206	122	1966	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.5243	77	1966	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.4256	116	1966	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.3509	116	1966	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	74.7029	88	1966	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	74.6658	55	1966	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:15:43,161] [INFO] DFAST Taxonomy check result was written to GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:15:43,162] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:15:43,162] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:15:43,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9960ebc2-441f-45d6-b24b-65684307df59/dqc_reference/checkm_data
[2023-06-29 16:15:43,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:15:43,223] [INFO] Task started: CheckM
[2023-06-29 16:15:43,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:16:34,989] [INFO] Task succeeded: CheckM
[2023-06-29 16:16:34,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:16:35,013] [INFO] ===== Completeness check finished =====
[2023-06-29 16:16:35,013] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:16:35,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:16:35,014] [INFO] Task started: Blastn
[2023-06-29 16:16:35,014] [INFO] Running command: blastn -query GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg9960ebc2-441f-45d6-b24b-65684307df59/dqc_reference/reference_markers_gtdb.fasta -out GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:16:35,852] [INFO] Task succeeded: Blastn
[2023-06-29 16:16:35,859] [INFO] Selected 22 target genomes.
[2023-06-29 16:16:35,859] [INFO] Target genome list was writen to GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:16:35,869] [INFO] Task started: fastANI
[2023-06-29 16:16:35,869] [INFO] Running command: fastANI --query /var/lib/cwl/stge56f5cc2-78a0-4d40-86be-275c1332c69e/GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:16:58,148] [INFO] Task succeeded: fastANI
[2023-06-29 16:16:58,168] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:16:58,168] [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_003388505.1	s__MB-PLM-1 sp003388505	99.9	1934	1966	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	conclusive
GCA_016795125.1	s__JAEUIG01 sp016795125	76.3828	213	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	76.3724	279	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610835.1	s__Planctomyces_A sp001610835	76.3306	203	1966	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_900113665.1	s__Planctomicrobium piriforme	76.2077	133	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669575.1	s__TH-plancto1 sp003669575	76.1985	60	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__TH-plancto1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671275.1	s__TH-plancto1 sp003671275	75.867	68	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__TH-plancto1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691905.1	s__SIAF01 sp009691905	75.7989	105	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	75.6474	80	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCF_007752535.1	s__Tautonia plasticadhaerens	75.6376	120	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235885.1	s__JACRIH01 sp016235885	75.4023	91	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACRIH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445035.1	s__UBA8437 sp003445035	75.3703	88	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872725.1	s__VGZC01 sp016872725	75.3274	62	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__VGZC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917235.1	s__QWPN01 sp903917235	75.1889	63	1966	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.02	96.87	0.85	0.84	3	-
GCA_016709225.1	s__Ga0077550 sp016709225	74.6935	88	1966	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
--------------------------------------------------------------------------------
[2023-06-29 16:16:58,170] [INFO] GTDB search result was written to GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:16:58,171] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:16:58,175] [INFO] DFAST_QC result json was written to GCA_937975615.1_SRR7515932_bin.106_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:16:58,175] [INFO] DFAST_QC completed!
[2023-06-29 16:16:58,175] [INFO] Total running time: 0h1m58s